"Replace existing" is used if you want your callsign to replace the existing FS callsign. The only reason for using "Replace existing" for a callsign is if FS contains a badly pronounced callsign.
As already suggested, the first thing to check is that you have the callsign defined for all 10 voices. If this is the case (as it appears to be here), try increasing the ATC speed (you can change it back afterwards). This forces EditVoicepack to regenerate all sound files. Without the speed change it will reuse existing soundfiles it already generated - good for speed, but not so good if there is a problem in the generated files.
If this does not work, check is if there are two copies of the file containing the voice file present on the system. P3d would then load two, and sometimes you would get the voice where EditVoicepack added your callsigns, other times you would get the default voice.
The easiest way to check this is to try to change the pilot voice. If you see two copies of each voice (so 2 x "Pilot 0 (male)" etc.) then there are two files. If you see this, please post here and I'll provide instructions on how to get rid of the extra file.