Dude, absolutely that could be causing your problems! Basically the wastegate opens at a set pressure, in the stock case its 6-7psi. It uses the vacuum line to trigger it.
If you have it hooked up right at the turbo outlet, which is how it it stock, the 6-7psi is what is right at the turbo outlet. Once you add an intercooler and have a pressure drop, your wastegate may be seeing 6-7psi, but instead of your engine actually seeing 6-7psi in the manifold, its likely more like 4-5psi. (Assuming a 2psi pressure drop across the IC) So technically with no other mods, you may be losing power by adding an intercooler. (granted the higher air density could offset this somewhat, but thats another point all together)
Now, by connecting the vacuum reference line to the turbo inlet, your wastegate will NEVER see the 6-7psi that it is designed to open at. It will only see vacuum. Therefore your wastegate will NEVER open. Which sounds like exactly the symtoms you describe.
Do yourself a favor, and if you are running an intercooler, reference the wastegate from between the IC and the throttle body. Then your engine will be seeing the same pressure of air after the IC install than it did before.
[ July 08, 2001: Message edited by: Drax240z ]