Regarding the serial issue... Are you using VISA or the "builtin" serial VIs? Are you using hardware flow control?
If you aren't using flow control, then it's very likely that the serial port isn't being serviced fast enough and bytes are being lost because of this. I think the "builtin" VIs (on the Serial palette) have problems with flow control. You could try turning them on, or maybe choosing a slower baud rate. The VISA functions do hardware flow control better, so you may want to try them instead. I'm not sure I understand the description of your second problem. I think Ben's thoughts about running low on resources might be relevant. I hope this helps. Brian