For 88.2kHz you need to use the --lax option (info: http://flac.sourceforge.net/documentation.html#flac_options_lax).
Dumb question: how do I do --lax with the FLAC frontend?
Or alternatively, how do I encode otherwise using command line?
Me not so smrt with computer.
It's explained at
http://flac.sourceforge.net/documentation.html#flacTo learn more about the details just click on [<general-options>], [<format-options>], [<encoding options>] there. It's actually a nice documentation.
Basically, if you look at your own screenshot you see which options FLAC frontend did use for you.
Example:
flac -P 4096 -b 4608 -m -l 8 -q 0 -r 0,4 myinput.wav
Now you want to add another option, in your case --lax. Some of the others also have different ways of writing them, e.g. instead of "-P 4096" you could write "--padding=4096" -- just make sure you know when to use "=" and when you don't need it, it's all under the [<x-options>].
So yours could be something like
flac --lax -P 4096 -b 4608 -m -l 8 -q 0 -r 0,4 myinput.wav
You don't need to specify an output file, standard would be myinput.flac (if your input file is 'myinput.wav')
Personally, I like to add the -V option so it verifies the encoding process for you, takes a little bit longer, though. Hope that helps (and works).