It is perfectly fine. The thing about portal files is that VHLT (the map compilers that come with J.A.C.K. and are the newest ones in general) generates some extra data in the portal file for its VIS to work. The problem is, J.A.C.K. and all other map editors don't parse this. If you open up the .prt file in a text editor, you'll see two numbers, and then a bunch of one-digit numbers afterwards, which is basically the thing J.A.C.K. is complaining about.
There's 2 solutions, you can 1) use Seedee's FixPrt tool or 2) use one of the modified VHLTs, either the latest version of Seedee's
SDHLT or my
ADMT.