yep sounds like the same thing thajeremy
As is often the case it was something I had done, so to help those who may do the same thing -
Some (Waves in particular) plugs always take about 3-4 minutes to load when opening pro tools, so when I’m tracking I remove all the plug-ins from the plug-in folder ( on my pc c:\program files\common files\digidesign\DAE\plug-ins ) and put them into a temp directory. So when I’m switching between programs pro tools loads quickly. When I’m mixing I put them back in and it rarely matters because I don't leave PT when mixing.
Turns out "consolidate" exists as a plug-in so if you remove every plug you've also removed the ability to consolidate your tracks. I had a look in the folder, but alas there wasn't a plug-in named "consolidate", so I haven't worked out which plug it’s a part of. So I just put all the plugs back and voila, consolidate is back.
FYI if you ever do the same!