What is your computer system and Firefox?

https://support.mozilla.org/en-US/kb/how-to-fix-preferences-wont-save

Note: Some software, like Advanced SystemCare with Surfing Protection, can protect files in the Firefox profile folder against changes. If you have such software then check the settings or uninstall this software.

Are you using Private Browsing? Nothing is recorded.

Hey thanks for the reply. I'm currently on windows 10 and running Firefox Portable 46.0.1. The portable is used to launch a custom web application. Here is the run down:

{

 "application": {
   "name": "Firefox",
   "version": "46.0.1",
   "buildID": "20160502172042",
   "userAgent": "Mozilla/5.0 (Windows NT 10.0; WOW64; rv:46.0) Gecko/20100101 Firefox/46.0",
   "safeMode": false,
   "updateChannel": "release",
   "supportURL": "https://support.mozilla.org/1/firefox/46.0.1/WINNT/en-US/",
   "numTotalWindows": 1,
   "numRemoteWindows": 0,
   "remoteAutoStart": false,
   "autoStartStatus": 2
 },
 "modifiedPreferences": {
   "accessibility.typeaheadfind.flashBar": 0,
   "accessibility.loadedInLastSession": true,
   "browser.cache.frecency_experiment": 3,
   "browser.cache.disk.smart_size.first_run": false,
   "browser.cache.disk.smart_size.enabled": false,
   "browser.cache.disk.smart_size.use_old_max": false,
   "browser.cache.disk.capacity": 358400,
   "browser.cache.disk.filesystem_reported": 1,
   "browser.download.importedFromSqlite": true,
   "browser.download.useDownloadDir": false,
   "browser.places.smartBookmarksVersion": 7,
   "browser.places.importBookmarksHTML": false,
   "browser.sessionstore.upgradeBackup.latestBuildID": "20160502172042",
   "browser.startup.homepage": "http://google.ca",
   "browser.startup.homepage_override.buildID": "20160502172042",
   "browser.startup.homepage_override.mstone": "46.0.1",
   "browser.tabs.remote.disabled-for-a11y": true,
   "browser.tabs.crashReporting.sendReport": false,
   "dom.apps.reset-permissions": true,
   "dom.allow_scripts_to_close_windows": true,
   "dom.ipc.plugins.flash.subprocess.crashreporter.enabled": false,
   "dom.ipc.plugins.reportCrashURL": false,
   "dom.mozApps.used": true,
   "extensions.lastAppVersion": "46.0.1",
   "gfx.crash-guard.d3d11layers.appVersion": "46.0.1",
   "gfx.crash-guard.d3d11layers.feature-d3d11": true,
   "gfx.direct3d.last_used_feature_level_idx": 0,
   "gfx.crash-guard.d3d11layers.feature-d2d": true,
   "gfx.crash-guard.d3d11layers.driverVersion": "20.19.15.4300",
   "gfx.crash-guard.d3d11layers.deviceID": "0x1916",
   "gfx.crash-guard.status.d3d9video": 2,
   "gfx.crash-guard.status.d3d11layers": 2,
   "media.gmp-eme-adobe.abi": "x86-msvc-x64",
   "media.gmp-eme-adobe.lastUpdate": 1463688058,
   "media.gmp-gmpopenh264.version": "1.5.3",
   "media.gmp-gmpopenh264.lastUpdate": 1463688059,
   "media.hardware-video-decoding.failed": false,
   "media.gmp-eme-adobe.version": "17",
   "media.gmp-gmpopenh264.abi": "x86-msvc-x64",
   "media.gmp-manager.buildID": "20160502172042",
   "media.gmp-manager.lastCheck": 1463688055,
   "network.cookie.prefsMigrated": true,
   "network.predictor.cleaned-up": true,
   "places.database.lastMaintenance": 1463497660,
   "places.history.expiration.transient_current_max_pages": 104858,
   "plugin.importedState": true,
   "plugin.disable_full_page_plugin_for_types": "application/pdf",
   "privacy.sanitize.migrateClearSavedPwdsOnExit": true,
   "services.sync.declinedEngines": "",
   "storage.vacuum.last.places.sqlite": 1463497660,
   "storage.vacuum.last.index": 1,
   "ui.osk.debug.keyboardDisplayReason": "IKPOS: System docked."
 },
 "lockedPreferences": {},
 "graphics": {
   "numTotalWindows": 1,
   "numAcceleratedWindows": 1,
   "windowLayerManagerType": "Direct3D 11",
   "windowLayerManagerRemote": true,
   "supportsHardwareH264": "Yes",
   "adapterDescription": "Intel(R) HD Graphics 520",
   "adapterVendorID": "0x8086",
   "adapterDeviceID": "0x1916",
   "adapterSubsysID": "06ff1028",
   "adapterRAM": "Unknown",
   "adapterDrivers": "igdumdim64 igd10iumd64 igd10iumd64 igd12umd64 igdumdim32 igd10iumd32 igd10iumd32 igd12umd32",
   "driverVersion": "20.19.15.4300",
   "driverDate": "10-1-2015",
   "adapterDescription2": "",
   "adapterVendorID2": "",
   "adapterDeviceID2": "",
   "adapterSubsysID2": "",
   "adapterRAM2": "",
   "adapterDrivers2": "",
   "driverVersion2": "",
   "driverDate2": "",
   "isGPU2Active": false,
   "direct2DEnabled": true,
   "directWriteEnabled": true,
   "directWriteVersion": "10.0.10586.0",
   "webglRenderer": "Google Inc. -- ANGLE (Intel(R) HD Graphics 520 Direct3D11 vs_5_0 ps_5_0)",
   "info": {
     "AzureCanvasBackend": "direct2d 1.1",
     "AzureSkiaAccelerated": 0,
     "AzureFallbackCanvasBackend": "cairo",
     "AzureContentBackend": "direct2d 1.1"
   }
 },
 "javaScript": {
   "incrementalGCEnabled": true
 },
 "accessibility": {
   "isActive": true,
   "forceDisabled": 0
 },
 "libraryVersions": {
   "NSPR": {
     "minVersion": "4.12",
     "version": "4.12"
   },
   "NSS": {
     "minVersion": "3.22.3 Basic ECC",
     "version": "3.22.3 Basic ECC"
   },
   "NSSUTIL": {
     "minVersion": "3.22.3",
     "version": "3.22.3"
   },
   "NSSSSL": {
     "minVersion": "3.22.3 Basic ECC",
     "version": "3.22.3 Basic ECC"
   },
   "NSSSMIME": {
     "minVersion": "3.22.3 Basic ECC",
     "version": "3.22.3 Basic ECC"
   }
 },
 "userJS": {
   "exists": false
 },
 "crashes": {
   "submitted": [],
   "pending": 0
 },
 "extensions": [
   {
     "name": "Firefox Hello",
     "version": "1.2.6",
     "isActive": true,
     "id": "loop@mozilla.org"
   },
   {
     "name": "Multi-process staged rollout",
     "version": "1.0",
     "isActive": true,
     "id": "e10srollout@mozilla.org"
   },
   {
     "name": "Pocket",
     "version": "1.0",
     "isActive": true,
     "id": "firefox@getpocket.com"
   }
 ],
 "experiments": []

}

I don't about portable, or if it's different from normal FF. I've called the big guys to help you. Good luck.

What security software do you have?

If you have TrendMicro software then try to uninstall the TrendMicro Password Manager via the Windows Control Panel.

Boot the computer in Windows Safe Mode with network support (press F8 on the boot screen or hold down the Shift key) to see if that has effect.

• http://www.bleepingcomputer.com/tutorials/how-to-start-windows-in-safe-mode/
• http://www.7tutorials.com/4-ways-boot-safe-mode-windows-10

I tried on a machine that has Avira (enabled + disabled) and I tried on a fresh machine that doesn't have any security software and the same problem arises :S.

Update. I solved the problem, there was a line in the Windows system file that was always setting it to private mode every time the program launched. Thanks everyone for their suggestions!

That was very good work. Well Done.