I would also think its very possible that she's pregnant... have a good look at her nips are they pink? I know you say you only let her out supervised, but even so it only takes a second, or an open window while your out for it to happen.

Its possible that as she is now the unneutered girl that she is deciding to become the dominant partner - which is going to take a few scuffles to sort out.

Another possibility is stress, if you are out alot of the time, and if she is as timid and worried as you suggest normally, then perhaps she is getting stressed when your not there. If the other cat is dominent then your presence could be stopping her from asserting that, when your not there they are fighting because there is noone to stop her.

Final possibility, is an illness - certain hormonal problems such as thyroid can cause behavioural changes, and these can only be diagnosed and treated by a vet.

I would be inclinded to pop her to the vets for a quick once over to check for anything that could be causing the problems. If she is only a couple of weeks pregnant its unlikely the vet can diagnose it better than you.

If given the all clear of illness's - get some feliway spray n plugins to keep the atmosphere calm, get a few new toys for them to play with and spend a little bit more time with each of them if possible.

It may very well turn out that she is expecting, if thats the case, have a read on the breeding forums on what you will need. Starting to collect a few cardboard boxes and newspapers wont do anyharm in the meantime!

Hope you get it sorted

xx