Ok, I got this:
Checking PHP version
[OK] PHP version is 5.2.x
Checking connectivity...
[OK] Can contact outside servers
Checking for SimpleXML module...
[OK] SimpleXML module exists!
Checking file hashes for corrupt or mismatched files
[Checksum failed] /install/navdata.sql did not match, possibly corrupt or out of date -- I didn't upload this when I just re-uploaded the install folder, no problem
[Checksum failed] /core/common/OperationsData.class.php did not match, possibly corrupt or out of date
[Checksum failed] /core/classes/ezdb/ezdb_base.class.php did not match, possibly corrupt or out of date
[Checksum failed] /core/modules/kACARS_Free/kACARS_Free.php did not match, possibly corrupt or out of date
[Checksum failed] /admin/maintenance.php did not match, possibly corrupt or out of date
[Checksum failed] /admin/templates/finance_expenseform.tpl did not match, possibly corrupt or out of date
[Checksum failed] /admin/templates/maintenance_changepilotid.tpl did not match, possibly corrupt or out of date
[Checksum failed] /admin/lib/phpvmsadmin.js did not match, possibly corrupt or out of date
[Checksum failed] /admin/modules/Maintenance/Maintenance.php did not match, possibly corrupt or out of date
Warning: file_exists() [function.file-exists]: open_basedir restriction in effect. File(/lib/js/jquery.form.js) is not within the allowed path(s): (/home/:/tmp) in /home/flynorth/public_html/pilots/install/checkinstall.php on line 140
[Error] /lib/js/jquery.form.js doesn't exist
Should I try re-uploading those files from the 2.1.928 update?
I just realised I re-uploaded the install folder from the 2.1.937 update ZIP, not the .928 one. I re-ran it and it only found the file I deliberately didn't re-upload because it was too big and would take too long.