Willi;
The problem is probably happening because the 6533 board doesn't have a deep onboard memory. Its on board memory is only 16 Words deep. Due to that fact, the data transfer to the computer memory relies to much on DMA transfers, meaning that the DMA channels need to be almost dedicated to that data transfer. Sometimes, other devices of your machine are using the DMA channels (the PCI bus has only 3 DMA channels that are shared in between all devices), so all channels are busy, and as you board can't store much data, you will loose some data points.
The safe way to go about this is to use the 6534 board instead. That board has a 32M deep on board memory, which will store data when all DMA channels are busy handling other devices' requests.
Hope this helps.
Filipe