While we didn't have the exact problem we did have a problem with that window. Ours fogged up. The only cure was to replace it. When we did remove the window I noticed the butyl tape had gotten hard and crusty in spots. It wouldn't have been very long before gaps appeared and water started leaking in.
It sounds like you'll need to remove the window and replace the butyl sealing tape around it. We used this tutorial to remove and replace the window.
http://www.rampknot.net/window_repair/AtwoodWindowRepair.pdfIt pretty much covers everything you'll need to know about removing and resealing it. Make sure you do it on a warm day. The butyl tape is extremely difficult to remove in cool or cold weather. Be extra careful when removing it if it's dual pane. You don't want to break the seal between the panes of glass and have it fog up.
It took about an afternoon to replace our window. It took longer to remove the butyl tape than anything else. We used a hair dryer to soften it up to make removal easier
