www.makemkv.com

I'm new to makemkv and need some direction. I'm attempting to create an mkv file for Thor: the Dark World (BD).

Scan the disc
Select a 27.3 GB titles.
Select the Title, Audio DTS 5.1, third Subtitles English & English (forced only).
Set MKV flags to "f" and observe MKV Flags: Forced in the Track Information
Make MKV

When I stream back the mkv file to my computer, using Media Player, when the dark elves speak, there are no subtitles.

However, with a Wondershare Player the subtitles are present. Therefore they must be in the file.
With a number of other BDs I've saved as mkv files, the subtitles have always been present when streaming with Media Player.

Additionally, where is information related to MKV Flags located?

What media player? Most standalones ignore the forced flag inside MKVs.

http://matroska.org/technical/specs/notes.html

You could try with both the default AND forced flags, that's what I generally do with foreign language tracks.

I have not found "forced" or "default" to be useful in a general sense. Best results are post-processing (with handbrake in my case, but other tools can do it, too) to re-order the audio and subtitle tracks to put the ones you want as default to be the FIRST FOUND. Want English audio and Forced subtitles by default? Those tracks need to have the lowest track number for their type, and most players will chose them.