HI,
reporting back with the solution that worked for me just to give closure to this issue in case anyone might experience the same.
It seems that for some reason, PFE is using PFE_FS9_Freq.dat when checking for current FSX frequencies which are produced by database rebuild.
Since I use FSX, the rebuild happens in the file labeled PFE_FSX_Freq.dat. When loading a flight plan it wrongly checks the FS9 variant of the file which was not updated by PFE because it reads out that the current sim is FSX.
Mainly I got different frequencies than those in FSX but for some airports, LGAV for example, none.
In some cases, with no freq to convert when loading a flight plan, in file freq_conversion.dat an error message appears.
The file can be opened with notepad by the way.
The solution was to copy and rename the file PFE_FSX_Freq.dat produced by database rebuild into PFE_FS9_Freq.dat and replace the old one.
This has to be done every time the database rebuild is run.
So, if you experience false freq in pfe or different than in FSX try this.