Not sure what might be causing the message to popup behind the main Window, but could be several things causing a hiccup in the file loading dialogs and the messages gets hidden. Couple things I would start with checking out .
I would guess the first part of the delay and most likely culprit causing the issue you are seeing is the paths being changed for your xrefs. Datacad is probably trying to resolve the missing xrefs. When an xref is missing from it's expected path, then it falls back to look for the files in a few other locations, for example the current file's directory. During this process, Datacad can do some decent processing, and that might be what causes the message to get hidden behind the main program window. Usually while this processing goes on, you might notice the title bar of the main program flicker. This is a good visual indicator that this hidden message issue may have occurred. I would guess you probably don't need to be waiting the 10-15 minutes, and that the orphan messages might be popping up sooner than that, but are just hidden behind the main Datacad window. Next time you notice the delay or the flickering, try using ALT+TAB to cycle thru your open programs to bring Datacad's Orphan message to the foreground. You can hold down ALT, and then tap TAB, to cycle thru the programs or use your mouse after the initial TAB when the multiple windows interface shows up . Sometimes switching to another open program and then back to Datacad will bring them to the foreground as well. These message usually get hidden when some part of a program or Windows causes the focus of Windows to switch to another program. You can also use the WINDOWS KEY+TAB to get a similar interface to switch between programs using the mouse.
As for updating the XRef and Image paths, the most straightforward way IMHO, is using the Orphan References manager to repath your missing files to their actual locations. You can find it under the Insert menu, Orphaned References.
Next, OneDrive. I am a OneDrive user as well and I would check in OneDrive's Settings, do you have File on Demand enabled? This stores all your files online, until your systems needs to access the files and then downloads them on demand. That download on demand process might be adding a delay or causing the 'hiccup' which suppresses the Orphan messages behind the main window. I would try disabling that setting if you have enough free drive space on your computer to store the contents of your OneDrive account locally.
Other things to check is what is your upload and download speed? If you are in the US, you should be able to use https://www.speedtest.net
to find out. Elsewhere, I am sure there might be other testing sites you could use outside the US if you are not getting good servers to test against.
All in all, you should be able to successfully use OneDrive as your default location, but you may just need to get your paths remapped in your existing files and maybe store your files locally in addition to OneDrive in the cloud if your bandwidth is an issue. This is how I use it. Everything syncs, but it writes locally first on each machine, and then updates the cloud. I like it this way also because it gives me a little more backup redundancy having the files on multiple drives / systems. If you get into trying to work with other users via OneDrive than you could run into some other issues, but that is a topic for another thread. Good luck and let us know how things go!