You have a very low counting rate but use DMA mode. DMA mode is recommended for high counting rates above 1 million stops per second. For your low counting rates please disable the "DMA Mode" checkbox in the settings. Don't use then the shortcut on the desktop for starting the server in high priority. When not using DMA, the server should run in normal priority.

In DMA mode the data transfer from the card works the following way: The software orders a DMA transfer from the card and provides a buffer address and buffer size. The block size can be set via the P7888.INI file, default value is 1024, for high counting rates of several MHz a value of 16384 is recommended. The card is then a bus master and usually signals to the software via an interrupt if the buffer is full. But with low counting rates a timeout will occure and the buffer will be emptied also if it is not full. The default value of the timeout is 2 sec. (In principle you can set a different value, for example 100 msec, by writing a line dmatimeout=100 into the P7888.INI file.) Each time when a buffer was transferred, the software checks if a time preset condition is reached. This will be in DMA mode and low counting rates only every 2 sec. So you observe always multiples of 2 seconds for the acquisition time with your settings.

Please don't use DMA with low counting rates. It is even dangereous as it is possible to get a blue screen if the timeout comes simultaneously with the interrupt (possible at rates of about 2kHz i.e. blocksize / dmatimeout).