phc, do you make use of the perspectives feature? One of the pieces of the information that a perspective preserves is how wide your columns should be. One possibility here is that some of your perspectives have column widths saved, and some are using whatever's been saved to the built in "default view" perspective.
I'd recommend you select Perspectives -> Revert to Default View from the menu bar, and then adjust the column width to whatever you prefer.
Next, select Perspectives -> Show Perspectives. When the perspectives window comes up, double-click the icon to the left of each entry in the list of perspectives at the left of the window.
That'll help you see which perspectives are causing your column widths and/or window size to change. Once you determine which ones are responsible, you can fix it, check the "Restore: layout" box in the perspectives window, and then select
Perspectives -> Take Snapshot of <name of perspective>
from the menu to save the new value. Hope this helps!