I use portable Firefox on a stick and also on a dual boot machine with a shared drive. Everything works fine except for one little annoying detail. Whenever I open Firefox in PCLOS I have to re-check the checkbox in options/advanced/general to always use autoscrolling. It stays set for Windows but not for Linux.
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Have you tried looking at the options in about:config as described here:
http://www.pclinuxos.com/index.php?option=com_smf&Itemid=26&topic=4175.m...
Also since this is an issue with Firefox and Linux, and probably not Portable Firefox, this forum is probably the wrong place to ask for that kind of help, but I hope this helps anyway.
Have an Awesome Day!