Ok, this is true in both Quicken and E-Sword for me, so let's see if I can explain it. (Using 11.1)
Both installed fine, both run fine.
I did make a copy of Quicken2012.app and esword.app and have put them into my Applications Folder/Dock. I start the application from the dock - it opens Crossover, it opens the app, all is cool.
There are the red/yellow/green buttons on the top left. I hit the yellow button to minimize the app. If I click on the tiny window representing the minimized app in the dock, it opens and all is cool.
BUT - if I have a minimized app (say esword), then click on the esword.app icon in the dock, the minimized app does reopen, but everything is frozen - the red/yellow/green buttons are all grey, and no mouse activity works. For I while, I just in frustration force quit, but then discovered another piece: if I go to the actual minimized app window and click on it instead of the .app icon itself, it "reopens again" and everything works.
Still, I'd consider this a problem, as in all my other apps, clicking on the dock icon.app reopens the app just fine.
Did this make enough sense? This is repeatable for me with two apps in crossover - so hopefully I've described it well enough to reproduce - but I'll be glad to say more.