Nothing with the config which suggests loading it directly in FS-UAE should cause any different behavior.
You should double-check that it actually opens in the same FS-UAE version as you use with FS-UAE Launcher. From the paths it looks like you are using OS X, and the OS X version of Launcher includes a bundled FS-UAE.app. Perhaps the FS-UAE you open the config directly in is an older FS-UAE version? (Please check fs-uae.log.txt)
If this does not explain it, please send two copies of fs-uae.log.txt to
frode@fs-uae.net, one after you have started the config via FS-UAE Launcher and one where you have started it directly.