Bought a '93 Tracker automatic back in April to tow behind our motorhome.  There was a little ATF underneath, but not that bad, and I wasn't too worried because I figured we wouldn't be driving that many miles, just towing.  Then when it quit moving, I added flulid and then there was a lot on the ground after driving.  It looked like the cork gasket was pretty wet so I went to this forum.  Someone on here said junk the cork and go to RTV, so I did.  Took my ATF bath, added a drain plug, applied Permatex RTV Sealant, bolted everything back together, refilled and NO MORE LEAK. Can't remember who gave the anti cork tip, but thanks whoever you are. A lot less painful than a tranny rebuild. Now if the RTV doesn't come loose and gunk up the transmission, everything will be great.

As long as you didn't just glob the RTV on there, it will be fine.  When I put RTV/silicone on stuff, I use my finger and put a thin even layer on...that way it doesn't squeeze/ooze out when the parts are assembled. 
Unfortunately, most of the time when I see where RTV has been used, it looks like they just globbed it on and used way too much.
Oh, and the filter and gasket kits I have bought for trackick auto trannys have always came with a rubber pan gasket.  So I just use it....no leaks.

Did you use the Grey Permatex ? That's the stuff for immersion in oil.

Works great for the engine oil pan too, the cork just splits and leaks
in no time, and is a PITA to change because you have to drop the
front axle just to get at it 

Wild 

I did use the grey.  Permatex does make a grey one especially for auto trans, but nobody carries it around here.  Package for the regular grey mentions auto trans pans, so I guess it is alright.  No leaks so far.