Ok. Attached (in the zip file) are t5.exe and its source code t5.cpp. This executable displays the same behaviour, but uses external gate (about 100 Hz) and internal source connected to the internal 100kHz. The output looks like this:
counter buffers before acquisiton:
counter 0 buffer begining: 0, 0, 0, 0, 0, 0, 0, 0, ...
counter 0 buffer end: ..., 0, 0, 0, 0, 0, 0, 0, 0
counter 1 buffer begining: 0, 0, 0, 0, 0, 0, 0, 0, ...
counter 1 buffer end: ..., 0, 0, 0, 0, 0, 0, 0, 0
counter buffers after 3000 ms acquisiton:
counter 0 buffer begining: 257532, 258537, 259541, 260545, 261550, 262554, 263559, 264563, ...
counter 0 buffer end: ..., 249498, 250502, 251507, 252511, 253515, 254520, 255524, 256528
counter 1 buffer begining: 616, 1620, 2624, 3628, 4633, 5637, 6641, 7645, ...
counter 1 buffer end: ..., 249494, 250498, 251503, 252507, 253511, 254516, 255520, 256524
Gil