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While capturing data with the ComProbe, it runs for a certain period of time, then stops capturing

Increasing the Nibble Delay usually solves this problem. In Serialtest ComProbe, go to Hardware Settings (in version 1.x this is under the File menu, in 2.x it is under the Options menu). The dialog box will look some thing like this, although your numbers will probably be different: 

Click on the "User" radio button and copy the values under "Computed" to the "User" column, but set the "Nibble" delay to half of the "Long" value. In the example above, you would fill in 20 for Short, 24 for Long and 12 for Nibble. Then rerun your test.