I just stumbled across this site in looking for some info on the (almost) exact problem.
I currently have an Omni II (no "e" or Pro), which I installed a couple of years ago during new construction of my home. I don't really have any "programs" or other stuff set up, other than custom naming all of the security points and an outside temperature monitor. I also started out with PC Access v2.x that came with the system when I bought it (through Smarthome.com).
I connect to my Omni II (when I do, which is not often lately) through a Windows Home Server and a Keyspan serial-USB adapter. I can Remote Desktop into the WHS, and then access the PCA software to pull up information on the controller - even if I'm away from home through the web-access feature on the WHS. I had originally tried a StarTech Serial-Ethernet adapter (to be able to access from my laptop on any network jack in the house) but could never get it working...and tech support didn't offer much help at the time (still hope someday I can make it work). Of course, at the time of my original installation, the IIe was not available, and the Pro was too much $$ for my budget.
Now, on to the problem I've been having (similar to the one posted). I'm still on my original firmware (can't recall the number), but recently upgraded to PC Access 3.0. Just today, even, I updated to the latest version available. When I log in to PCA3, and load an image file, and then try to connect, I get the "no reply (1)" message. If I generate a BRAND NEW file, and then put in the master code and try to connect, I connect to the controller just fine. I can download, upload, etc. But as soon as I save, close the program, and then re-open and open the file, I can no longer connect.
I still have v2 of the PCA software on my computer, and if I try it (with the pre-v3 file), it connects just fine. And if I have the log/config program for the keyspan adapter up and watch it while trying to connect with the PCA3, it shows it makes a connection and then closes the connection almost instantly.
I had hoped that maybe upgrading to the new 3.0 firmware would help...but in seeing this post, it looks like probably not. So now I'm stuck wondering how to make it so I can reliably connect with PCA3 (which has a MUCH nicer interface) so I can actually start tweaking and programming this thing beyond the basic setup I have now. I really don't want to have to upgrade the controller to something else until some day when I am ready to fully integrate it into the home network, and run it off of the WHS console add-in or something...
Any ideas/help you might have to offer is greatly appreciated.
Edit - oh, one more note - this problem has persisted through every version of PCA3 I've updated to...