The conversion to .idml is unlikely to be the cause. More likely are Live Screen Drawing, cross references, link previews, live preflight, or something similar.
What was added t the file in CS5.5?
Thanks - good call. It was due to the fact I had a whole pantone colour library imported, I deleted the swatches and it is now working fine.
A WHOLE Pantone swatch library? I didn't think ID would let you go beyond 10 spots without complaining very loudly, or was it a process library?
I'm not going to ask why. Well, yes, I am. Why?
Ha - just lazy, I guess!!
It was a process library - I find it easier to just select a colour from a whole library (similar to what you would do in Photoshop) rather than having to go through and add a new swatch each time. Probably a bad habit, and you are right - ID doesn't like it much...!