that said, problems seems not to be related on the merging of files but more on a missing property needed by Many Faces of Go.
Here is what I did :
- dowloaded and installed "Many Faces of Go" trial version 12, later refered as "MFG" in this post
- dowloaded qjzm.zip and extracted files to a directory
from there, I just renamed one of the file from "qjzm1-1.sgf" to "qjzm1-1.prb".
I opened "qjzm1-1.prb" using the menu "File"->"Open/View/Edit Game"
then play then correct move for white and MFG told me that was the wrong move... then asked MFG to tell me what was the correct move and it showed me the same move I just played...
I then looked at another problem file that was part of MFG distribution (C:\Program Files (x86)\Many Faces of Go 12\Problems\lvl0.prb"
and that file worked fine...
so went back to the file qjzm1-1.prb and looked at its content .
The content was a valid sgf file.
I then watched at diffrence between "lvl0.prb" and "qjzm1-1.prb" and found that there is a "TE" property in the working file. (in sgf, TE means for TEsuji move)
I then added that property to qjzm1-1.prb
and that change made the problem working right on MFG.
Unfortunately, that will not help you much... that just tend to indicate that MFG may rely on TE property that is not present in all files...
[edit]corrected some typo[/edit]