On upgrading, if these are Flac files there shouldn't be any issue .. if there are wav files some of the tags can't be written to the file. Also you have library backups so the data should not be lost. Now if you are upgrading from one version to the nex, you should leave the old version on. The library of the previous version (19 to 20 not necessarily 17 to 20) will just port over seamlessly (or should). If you remove the prior version and reimport the songs into the library, non-embedded tag information will indeed seem to disappear, because it is just not there. Thats why if you are not keeping a prior version when you up grade you should just restore the "final" backup to the upgrade.
Now on rebooting? That's something else again. Thats not good. Not sure why that would happen. . If the tags are in the library, the tags just wouldn't disappear as they would not be reimported.
What format are these ripped audio files that fail? You might want to check to see if they are corrupted. If you want I can post a tool that can check the files. I would make sure the information can actually be stored to the files and is indeed embedded (in options) as a double security until a solution is found.
oops I see Marko has asked the good questions while I was typing