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

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