What could be helpful in your situation is to run the capture software on high priority. Like this, it should record continuously without dropping frames because it will basically own the CPU and I/O. If your HDD is not the greatest, consider using the lossless Huffy video codec to capture to. That will cause less demand on the HDD than uncompressed.
In any case, keep the HDD defragmented as much as possible, especially before going to capture.