Is the fluid at the correct level,not over full?
If so,you may need to be careful using this stuff.
A trans. valve body has several small passages,not to mention other tricky parts.
It may be possible for this stuff to accumilate and plug something that it shouldnt.
If you cant replace the seal.
Try changing out the fluid and filter.
This should get some of the stop leak out.
After this,refill to the proper level,you should be able to use the stop leak again,just be sure to keep an eye on things.
It is also possible that the seal has gotten to the point that stop leak wont help.