a/ I assume you have the lastest available version of PAF5 - i.e. Version 188.8.131.52.If not, you should upgrade. There were a lot of bugs in some of the older versions.
b/ I assume that you have run the "Check/Repair" procedure under the main menu "File".This procedure will usually detect file errors. It is best to run it as a "Check" only first, then if it shows any errors, inspect each entry to see if you can find out why there is an error. Try unlinking an individual from his "correct" parents and then relinking her/himagain. It is best to proceed this way since using Check/Repair may cause other problems. Run Check/Repair only if you feel that you cannot find any way to manually fix the problem.
c/ I assume that you have run "Possible Problems" under "Print Reports - Lists".If the problem individuals show up in this list investigate why and correct.
d/ I am also curious as to what you see when you open a problem individual, then click Edit - Parents.It should show only one set of parents, relationship "Biological".If other parents show up, make sure the biological parents are "Primary". Investigate and clear any other "wrong" parents.
e/ If none of the above indicate any problems, then you may have to "reload" your file.Make a backup of existing file.Run an Export on existing .paf and save the created .ged file under a new file name. Create a new (blank) family file (File- New - new-file-name).Run Import on the .ged file previously created by running Export. PAF should load newly created family file and report any problems it had while extracting data from your .ged file. Check to see if this fixes your issues and investigate and fix any problems reported during Import.If problem is resolved, you may want to delete any old .paf, .ged,.zip files to avoid confusion.