I found a work around, as it seems chrome insist on using profiles (which I do not want) except when in incognito mode but this does not solve the my issue of the self deleting shortcuts.
Launching chrome.exe with a few switches pretty much "solved" my issues.
chrome.exe --profile-directory= --incognito --disable-session-crashed-bubble www. my-homepage .com
--profile-directory= leaving the profile path blank solved the deleting shortcut issue but brought two more.
1. On exit a crash notification will always popup, using --disable-session-crashed-bubble will prevent that.
2. On next launch a restore session will always popup --incognito seems to be my only work around for this. www.my-homepage.com forces a homepage when using --incognito
Unfortunately Chrome is still very flaky in our environment. I'm still testing, if I find anything worth while I shall post. Hope this helps someone.