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Hi. I'm the author of BD3D2MK3D. It's the first time I heard of this problem. Retrieving the audio delays should not take longer than a few seconds. The operation that follows immediately is the extraction of the 3D-Planes from the MVC stream, but it is skipped if no subtitle stream has been selected in the second tab. Then, the subtitles are converted to 3D (again only if necessary), and the audio streams are converted to AC3 or AAC if you have requested that option. Finally, the scripts necessary to encode the video and mux the final MKV are generated, but that takes only a few seconds.
I suggest this: Untick all subtitle streams in tab 2 as well as the "Convert the audio tracks" option in the same tab. That way, the scripts should be created immediately after the retrieving of the audio delays. Be sure to open the console (via the menu File -> Show Console), and retry. If something goes wrong again, copy the content of the console (especially the last lines) and paste it here (or just paste the content of the BD3D2MK3D.log file, that should have been created in the project folder). I'll try to help.
If everything is OK, restart again, this time with the options you really want, abd be sure to not use your PC for another job during the preparation of the project, and let me know if it worked.
Sorry, I can't help much more.