It's not VFP, me but might hit you one day too. I have all 3 on same computer, shortcuts side by side.
I had a form that I'd modify. Before modification I wanted to run once to see where I left off yesterday and got error on line :

lnCaptions = alines(arrCaptions, ...

It was saying 'variable arrCaptions not found' and alines wasn't syntax colored. I was stumped at first but it ddn't take long to realize I was running under VFP5 :) Switched to VFP6 and same error message again, and yep it wasn't syntax colored. Story goes on like that. To keep it short solution was :

compile form myForm
compile class ClassName && for all classes used in form

On first run under VFP5 it compiled behind the scenes but VFP6 was directly using VFP5 compiled code w/o recompiling.
Cetin