"Firstly, the text/fonts just don't look the same. Everything has been designed using Ariel (no fancy fonts), on the PC the text is thinner but looks wider, bold is fatter too. This appears to be clipping the text and needs the borders making larger for the text boxes."
Yep, that's a known difference between the two operating systems. WIndows machines need a tiny bit more space to display the same text than Macs. Fortunately, once you adjust all your layout text and fields on a windows platform, the layouts will usually work just fine when you take the file back to your Mac. When developing on a Mac for an FMP file that's going to be used on Windows, I've learned to leave my self an extra bit of space in my layout designs and then I flip through each layout once on a windows machine to check for any needed adjustments.
"I have written scripts for a button to open up a new window and go to a particular layout, when the script runs the main window stops being maximised too (this doesn't happen on the Mac)."
This is a known/reported "windows" bug. I can minimize, but not eliminate the "twitch" if I add a few extra windows management steps to my script:
Right after a New Window, or Go to Related Records (with new window option) step I put in:
Move Resize Window [Name: Get (filename); Current File; Height: get (screenheight); Width: (screenwidth); Top: 0; Left: 0]
Once a new window is closed, I add: Adjust Window [Maximize]