Thanks for the link and help there chaps. Our genius IT guy sorted the conversion to XPM thing out. But since he just typed furously in the Linux console I have no idea what he did!
As for the window issue... well it's still a bit of an annoyance, but I managed to tweak the 'advanced' window settings to remember the previos sessions setting. So now my Outliner and Hypergraph etc don't just ping behind Maya's main window when I click on the viewport.
It's been a week on Linux now and I'm still far from comfortable. One reeeeeeealy annoying thing was the 'kate' text editor. I'd make some changes to Maya shelf file and overwrite the original. Open Maya and to find the changes were not made. So I'd re-open the file in 'Kate' only to find that the chnages were not saved! I think it was someting to do with the way Kate has 'sessions'... great for people that are totally plugged into the machine but I want a simple text editor!!!

When I save a file I want it to stay saved!
Rant Over.