So you have 3.1 roms and you're running workbench 3.0. Right?
3.1 seemed to be quicker with its display, as I think the graphics.library was different. Also the monitor drivers are different.
Otherwise I can't think of any patch that REQUIRED workbench 3.0 as opposed to 3.1. Most things off aminet specified 3.0/3.1. In fact some 1.3/2.0 stuff that didn't work with 3.0 worked with 3.1. On the whole, I've read 3.1 is MORE compatible than 3.0, So you should be Ok just installing 3.1 over the top.