1 minute 50 seconds was with an empty project! I don' know. Everthing seems freezed.
1)
Does the message window say anything about building packages, such as LCL?
This could be if something went wrong, and the IDE thinks you changed options for packages, or if timestamps on disk got messed up.
You can check (before pressing build or run) under menu: View > Ide Internals > What needs building.
2) When you press run, the following step are usually performed:
2a) Compiling of your project
2b) Linking (this is shown in the messages window)
2c) starting GDB, and getting it to run your app
2b can get really slow, if you have not enough memory.
This is especially true, if you use smart linking.
2c can be measured, if you first "build" without running, and then "run" the project.
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If you also use FPC trunk:
IIRC there recently where reports about problems building lots op packages. (I think on the mail list). I don't know what caused the error, but maybe it is related.
It may be worth testing with 3.0.4 (and/or up/downgrade the svn version of fpc)