Always boots to coherence from apps in the dock

I upgraded OS X from 10.4.11 to 10.5.1, checking the forum beforehand to see how this might affect my installation of PD 2.5 build 3120 (which I was content with, didn't want the 3.0 features). Saw there was a build 3224 for 2.5 on Leopard, so downloaded that.

Now that I have installed both, behavior isn't the same. I prefer Window mode, not full screen or coherence. My VM run Win2000 SP4, and I use one Windows app. Quicken 2007 Premier. Before the upgrades, I had the Quicken app in the dock. Clicking the icon would start the VM in window mode and open Quicken. The first time after upgrade, I couldn't use the Quicken icon in the dock, it just displayed a question mark on the icon. So I removed it from the dock and started it from the VM and then set the running icon to keep it in the dock. Now if I open Quicken from the dock, it always wants to start in coherence mode.

I've tried everything in the User Guide. Tried setting the booting options in the virtual machine to Windowed. Nothing helps. If I just start the VM, then Quicken from the Win2000 desktop, it performs as the settings. But regardless of any setting, if the app is started from the dock, I get Coherence.

This is on a MacPro, 2x2.66 dual-core Intel, 2GB of RAM, two 160 GB drives(RAID) and two 250GB drives(RAID). No Boot Camp.