Adjusting Eclipse console size
Right click on the console > Preferences > Console buffer size
If you don't want any limit, uncheck the "Limit console output" checkbox.
Mine is currently set to 800000, which is enough.
In Window > Preferences > Run/Debug > Console
, there's a checkbox "Limit console output" and a text field for entering the buffer size of the console.
Have never changed those settings myself but sounds like this could be what you are looking for. I am using Eclipse 3.3.2.
I had a similar problem with my c++ build console. This is set in Preferences->C/C++->Build->Console