The settings explained:
Quality (compression level)
I think the name of this setting is a slight mishap and can be misleading. The same setting in the Monkey's Audio encoder plugin is called "Compression Level". Perhaps JRiver could change the displayed name.
If I recall correctly the default compression level value is 6 and I think it is pretty much optimal for general use. 7 & 8 compress only very slightly more and are slower. If you find the level 6 too slow you can try a smaller number.
The level 0 is very fast but the resulting file size is a lot bigger. I have used it for saving temporary files when I want to convert a bunch of files to an intermediate lossless format before editing them with a wave editor.
Verify
This compares the decoded PCM data and the encoded FLAC file during the encoding process. You can use it, but because it does not redecode the source file it can verify only the latter part of the process. I don't think it is necessary unless you suspect hardware problems.
Add 4 k padding block
Reserves some empty space for the file tags. It is a useful setting. The FLAC tags are stored in the beginning of the file and without adequate padding a tag change can trigger a complete rewrite of the FLAC file. This setting can speed up tagging only when you are storing textual metadata. Cover art files don't usually fit in the reserved padding block.
Add seek table
Makes seeking faster. Keep it enabled unless you have a specific reason to disable it.
Use Ogg as transport layer
This packs the encoded FLAC audio stream in the Ogg container. Use it only if you need to create Ogg-FLAC files for an external application. MC's Ogg decoder supports only the Vorbis format.
