Hi Frank...
Your Windchill environment must be set up wrong. Although I often use the checkin tools directly from Creo, I do not have any issues with the workspace checkins.
You have multiple things going on. First, when objects are being modified even when you didn't touch them, there are some known causes and solutions for this. I'd need to discuss this more to figure out what's exactly happening but in 95% of the cases, I can fix this.
If you stick to simple interactions with Windchill, you should have few problems. You need to keep up on workspace maintenance. This means keeping your cache cleared, emptying your Event Manager (or setting it to self-clear), updating out-of-date objects, and occasionally synchronizing with your Commonspace server. In addition, you should cycle your workspaces at least once or twice a month. You don't want to keep using the same one for months... that's just inviting trouble.
I suspect with a few tweaks, we can get Windchill working to where it's not such a big obstacle to your work. I deal with a host of user issues on Windchill every day. Most of those problems are due to the user not interacting with the system "correctly". I realize that's a loaded term... if the procedure for doing a certain action is convoluted or confusing, it's tough to know what the "correct" way to use the system is.
A small portion of the problems are due to configuration issues. An even smaller bit is due to administration issues... for example an Oracle server that's not properly tuned or optimized... or a Windchill application server with too little RAM or too few method servers running. I can help with this, too... but we'll probably need to talk offline. I doubt I can work through all of this in emails.
Get in touch with me using my work email and let's discuss this further. I'm sure I can help alleviate some of the problems you're seeing and ease your frustration a bit.
Thanks!
-Brian