Start Firefox in Diagnose Firefox issues using Troubleshoot Mode to check if one of your add-ons is causing your problem (switch to the DEFAULT theme: Tools > Add-ons > Themes).

See Troubleshoot extensions, themes and hardware acceleration issues to solve common Firefox problems and Troubleshoot issues with plugins like Flash or Java to fix common Firefox problems

See also http://kb.mozillazine.org/Preferences_not_saved

has not helped... autoscrolling is disabling also in safe mode(with disabled plugins), and user.js doesnt exist (so it shouldnt cause problems)

Are you having the problems with the setting in Edit > Preferences > Advanced > General: Browsing: "Use autoscrolling" or with clicking with the middle mouse button to enter auto scrolling?

See also the middlemouse prefs in http://kb.mozillazine.org/Category:Preferences

It is possible that Ubuntu has changed some settings in its Firefox version.
You can try the regular Firefox version from http://www.mozilla.com/firefox/all.html to see if that works.

problem is with settings - its turning off, not with autoscrolling itself...

I've tried the "regular version" (uninstalling firefox and its ubuntu support packages and then using the downloaded one) - it didn't work

Thanks for the pref pages, I tried to compare prefs.js after using in windows and linux - everytime after using FF in windows one line (user_pref("general.autoScroll", true); ) is deleted. But still I dont know why its being deleted and I dont understand why the autoscrolling is everytime turned on in windows although the setting is deleted... Any ideas?

I think I will write some application for launching FF wich will everytime add that line to prefs.js

Anyway thanks for help

/edit solved by using c++ script