Had similar problems awhile back with a Warp13a. Had CPU temperature, memory, etc. monitoring software running in the background that would interrupt the process every couple of seconds. Thing would work great for weeks on end, then die, only for me to have to trouble shoot it for days on end. Turns out, every once in awhile, the wife would reboot my laptop and re-start all that monitoring stuff, thereby causing me to lose my mind for a few days.
Another issue I've had in the past is hubs. Seems like my programmers have never liked to be on a hub, powered or unpowered. You might not have enough juice to push the programmer (i.e. USB port not completely 100% powered to 500mA like the spec says, somebody check my values here).
Maybe try a powered hub?
Something else that affects RS232...a continuous ground between everything. Some have it, some don't.
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