That kind of thing is what IBController is designed for. I still have the "Tip of the Day" dialog enabled so it comes up every time TWS starts up and I see IBController dismisses it. That window can be disabled in TWS but I'm just lazy. IBController is opensource (on SourceForge) so any Java programmer could add code to do the same thing for the window you want to auto-dismiss.
I gave up on java on Ubuntu 10.04. TWS and Ameritrade's Command Center app kept on killing the window manager. I now run them in a Windows XP virtualbox session. Virtualbox has a nifty feature where it can hide the Windows desktop and show your Linux desktop, so it's almost like having your Windows apps and Linux apps running side by side.
I had been running the OpenJDK java vm for awhile but recently switched to the Sun java binaries because my system was bogging down at times. I have found since that the Sun jre takes around 30%-50% less CPU at any given time than the open-source one. It may not be noticeable if you run only a few things but if you have a desktop that is doing other stuff you may want to just install the Sun jre and change the script that calls TWS and see if that lessens the load on your system. For the most part, TWS has run very well (even with OpenJDK) on Ubuntu 10.10 and 11.04 except for the minor CPU hogging when the market was really busy. The Sun binaries seem to have corrected that and other than having to run my trading app in Wine which has its own set of challenges I really like using Linux as a trading PC. For the record, Xubuntu 11.04 w/ XFCE light-weight desktop is a really good choice if you are turned off by Unity and Canonical direction with the mainline Ubuntu distribution.