That's a known issue with TMS when you have a large number of modifications.
You can turn off the "Careful Rebuild" option, but it will mean that you'd have to do a manual rebuild when you make changes (I think). But that's only an issue for us now that 1.1.4 has the white screen of death sorted. So the idea would be you make a load of changes then manually kick off the rebuild when you're done, I think.