I had a problem like this a while ago when I switched VISA versions on a computer.
I eventually got it to work by wiring a -1 to the DTR line instead of 0. Don't ask me why it worked, it just did. I have asked in the serial forum why this is, but I've never heard a reason.
As far as I know, -1 is simply an unknown (maybe uncontrolled) state whereas 0 forces 0, and 1 forces 1. Perhaps -1 allows other software / hardware to still take control of the DTR line. Your guess is as good as mine though.....
Give it a try.
Hope this helps
Shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)