There isn't any "flushing" of macros when saved, and I'm not aware of an timing problems. System macros never get saved by VBP itself anyway.
You might try downloading and re-installing from
http://www.kinook.com/Download/VisBuildPro57.exe. There was a patch for a bug where global macros on a network share were not always saved properly (although this wouldn't affect system macros so I doubt it would apply in your case).
Could you send your .bld file to
support@kinook.com, describing exactly when and how things go bad when this problem occurs? Something about your project might stand out as something we could mimic here and try to investigate. Thanks.