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1) if the check says that there not there, then they are either missing or they are the wrong files (e.g. from a previous version).
2) In some cases this is OK. For example:
a) you have installed XOOPS and the check shows that the files in /install folder are missing. This is OK, because the /install folder has been renamed to something different (e.g. /install_acoh9909809)
b) you have moved the /xoops_lib folder somewhere else, and/or renamed it to a different name.
c) you have updated the mainfile.php files, but the filecheck might flag it as missing because it is different from the original
In all three cases the file check will list all the files in the original /install and /xoops_lib folders as missing or invalid, but you can ignore it.
All other missing files should be taken seriously and if needed, you should download them again.
As a general rule, the checksum should be run BEFORE installing XOOPS.I suggest to read the
Installation Guide, and follow it.