I have a 4640 streaming FLAC files from my server (via Plex). I'm wondering if the Roku ultra is doing some kind of transcoding to the audio however. My DAC shows 48Khz LPCM which makes me think it's taking the 44.1Khz original file and transcoding somehow. This particular version of the Ultra seems to kind of transcode a lot. For instance it takes DD5.1 encoded video files and transcodes to DD+5.1. There's definitely something going on there. Anyone know? Thanks!
As far as the DD to DD+, yes the 4640 is the only player that has a Dolby encoder, so it will upconvert DD to DD+. Not certain of the benefit, but it does it anyway. I've never played with different audio codecs, so can't say for certain what it might be doing. It's also possible the Plex server is doing the LPCM conversion. You might ensure Direct Play is enabled for playback.
I checked the official Roku media support page, and they don't list anything specific about playing FLAC files. But that might be the way they support FLAC, by converting it to LPCM.
48kHz LPCM is a lossless representation of a FLAC file.
The FLAC format can not be transmitted as-is over the optical cable as the S/PDIF standard does not mandate it's support. Also, the TOSLink standard is just a single fiber resulting in one-way transmission. Unlike with two-way communication standards such as HDMI, the media player can not get any information for the receiver as to it's capabilities or verify it has changed modes correctly. It is easiest to confirm compatibility across the largest number of audio receivers by fixing the sample rate at the S/PDIF default of 48kHz. Trying to support the optional S/PDIF sample rates of 44.1 kHz and 32 kHz adds complexity while not having a noticeable improvement.
As to the question of transcoding, going from FLAC lossless compression to LPCM raw uncompressed format is transcoding but still remains lossless. Going from 44.1kHz to 48kHz is considered up-sampling which is a modification but does not produce anything close to the undesirable effects of digital audio compression artifacts.
If you have a computer with a premium sound card that includes a TOSLink audio fiber connection as an option, I recommend trying to see if you can get the sound card to transmit to the receiver at the 44.1kHz sample rate. I would then try playing the same FLAC file at 44.1kHz PCM and see if you can hear a difference between sample rates. Preferably try having someone else choose the sample rate randomly without telling you ahead of time so you are doing a blind taste test. I personally can't hear the difference with up-sampling but I can hear the impact lossy compression formats like 128kbps MP3 has on several audio samples.