Transmission Problems on 1999 Beetle

So in addition to the many other problems people have mentioned I think I might have a transmission problem.
My car sometimes has trouble switching gears. When I am at a complete stop and go from stop to go sometimes i pauses, almost stalls, keep in mind its an automatic, an than jumps forward. In addition sometimes I feel as though it takes longer than normal to switch from 2nd to 3rd etc.
So we take it to our normal mechanic who takes it to a transmission specialist who says because of metal in the pan and burnt fluid he thinks the transmission needs to be replaced.
Since we have the 100.000 mile warranty we take it to the dealership. The dealer than calls us back saying they don't think it's the transmission but fluid was leaking and stuff which will cost $500. He doesn't think it's the transmission but to test it it will cost $200, which if it comes back positive they won't make us pay for the test and will replace the transmission, but if it comes back negative will make us pay the additional $200.
Here's the key part our car has 99,000 miles.
Do you think the dealer is just trying to screw us out of replacing is by saying he doesn't think thats the problem hoping if the problem continues by the time we get the car back it it's past the warranty?
Does anyone know about transmissions? Is it just the fluids?

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-Nina