I was fighting with a lot of problems with MiKTeX lately, and in the run of that had about three different installations. While the updating process and package selection might have been a tad dfferent in these instances, they were all based on the 2.9 portable package and updated regularly. One day I realised that these installations had different contents in the miktex/bin and miktex/bin/internals directory. One installation was missing the bin/mpm.exe. Another one was lacking copystart.exe, copystart_admin.exe, miktex-update_admin.exe, uninstall.exe, uninstall_admin.exe and I believe at least some of the run(xy).exe files. (I found these partly in the miktex/bin directory, but alas, my notes aren't complete on that.) I thought this could possibly have a connection with the "update helper not found", "package management utility could not be found" and related errors.
Therefore this feature proposal:
It would be good to have one method of checking for completeness of the base installation. Ideally, starteable from the tray. I'd also go with a list of files as a text file somewhere, so I could check myself.
If there is a "file not found", it would be good if MiKTeX could somehow signal what file it looked for and, ideally, where.
(I tried to find out with the Execution Trace, a host of streams selected, "access" among them, but that didn't show anything. I'm exploring other possibilities, but I really believe that could be made easier by just putting that info in the relevant error message.)