Version 1.925 released on 5-25-2013
◦ Entities: IMPORTANT! Fixes a really bad bug where outputs would be lost when file is closed. To get this fix, you need to download the latest version then go to the WW Settings dialog and click the Reparse button near the FGD list.
◦ Entities: Version for entities at 14.
If you have already closed a file with outputs in the last few days, the outputs may be lost. Applying this fix and reparsing your FGD (if you already used the entity tools before this release, will fix future uses of the entities.
And following this I found the same problem with spawnflags. 1.9252 fixes that too.
The best thing to do it this:
Close Max.
Download the update.
Open Max.
Go to Wall Worm > Wall Worm Settings
Click the reparse button.
Now all new entities will save all data correctly.