Password stored not filled in

Hotmail does the same to me, I believe this is a "feature" of the Hotmail site itself rather than a failure on the part of Firefox. If that is true then there isn't much that can be done about it. In any case, AFAIK it's not a problem that occurs only with the Portable version (please correct me if I'm wrong), so it's something to address with the Firefox developers. Although, as I suspect they will tell you, there's nothing they can do about it.

Keepass is a good alternative, I use it a lot and you can force it to use certain username/password combinations for certain sites (where it might get confused and try to use the wrong one like Firefox). In that sense, it's more flexible than Firefox, and it also supports custom form completions such as with your Internet Banking where they may require additional information/fields beyond username and password. In addition, the form completion for Keepass is only a global hotkey away, it works very well.

this is the best to start with if you want have it correct.

Then start again.
But note that as mentioned, some sites have 'feature' that they can not remember the password even if this is explicitly ticked, e.g. hotmail.

some sites load the whole stuff for authentication from other part and all is changing so much that FF can not understand which personal data to put in. This is quite usual and probably can not be solved so far.