I've tried to startup Liferay IDE 1.4 eclipse bundle on Ubuntu after starting up application server from the console.
Starting up from the command console for the first time created some properties file as well as data directory in my Liferay application server installation.
When I tried to startup the server from Liferay IDE 1.4 afterwards, it throws some errors about the properties files.

It seems Liferay IDE does not recognize properties file created by portal-setup-wizard.properties because there are some values with spaces.

I was able to get Liferay server started from IDE by deleting all the properties files and data directory that were created during the startup from the command line, but wondered if any one else has encountered this problem and if this is a bug in IDE.

EDIT: I may have been wrong. I'm now getting com.gerninus.easyconf.AggregatedProperties errors. I'm also not able to connect to remove Liferay6.1.0 Tomcat bundle server. Seems Liferay IDE 1.4 doesn't support it yet. I'm begining to have a very strong doubt about Tomcat 7 actually supported yet. I haven't had any problem with Liveray 6.0.6 Tomcat bundle using Tomcat 6 so it seems it's an IDE 1.4 error with Tomcat 7.

EDIT:Got it to work by downloading Eclipse and adding the IDE plugin separately. No problem this time.

Thanks for this report. There very well may be a "spaces in the path" error with the new tomcat7/liferay6.1 support. I'll take a look this morning and report if I find anything.