Can you see the paypal transaction ID's? it will be in the payment notification email.
Then contact paypal with the transaction ID's.
Had a similar issue with paypal about 5 years ago i think. Its when they started holding payments. I had about 10 or so payments that got released from the pending balance but then disappeared and didnt appear in my available balance. I was doing big numbers and hadnt noticed until my figures didnt add up. Contacted Paypal and they then had to 'find' the payments and 'manually release' to me. I wonder how much money went 'missing' like this and no one noticed. This totalled about £2k for me.
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