I have made some progress, but now am more confused than ever. I found an old program called "ATsend.exe" that works through DOS. The commands are atsend [string] [com port] (example C:\atsend H0 3). I created a batch file to run all query strings and placed it on the customer's desktop. It works fine, although that did not fix the problem. For some reason there is something about querying the modem that "wakes it up" which this program doesn't do.
***Simple layout of my problem***
software 1 tranfers and receives from time clocks and can transfer at any time.
modem string from software 1 holds open modem port and does not free up for software 2.
software 2 cannot transfer if software 1 has transfered at all until modem has been queried or the machine has been rebooted.
Turning off the modem for awhile and turning it back on does not help.
...confused yet? Thank you for any help guys, I know this is a whopper