Last night playing with versions of SC and found that earlier version of Squeezecenter 7.3.1 - 24372 @ Fri Dec 19 17:30:38 PST 2008 (and earlier) WORKS fine with flac and cue-sheets.

Later versions that I tried were:
- 7.3.2, 
- 7.3.3 (squeezecenter-7.3.3-24744) 
- 7.3.4 (squeezecenter-7.4-24746) 

All of them had the problem -- flac+cue sheet duo didn't work.

QA to verify

Eugene, the version of SoX that that you are running on your QNAP needs to be updated to include FLAC support.  This is required as a result of change 24410 for bug 9997.

Thanks for the info, but can you please give more details (the link, how to, help file, fm to read through,  etc) on how to do update the SOX and to which version? Isn't it a part of SC?

Steven: Can you provide instructions on our Wiki to do this please.  Then point Eugene to the wiki page.

Here's some additional info on the issue from forum topic (user flipflip):

>Yes, the version of SoX in SSODS is compiled without FLAC support. This is because I was unable to 
>compile it with FLAC. And then I thought "who cares?" because the SC plays FLAC natively (doesn't it?)
> and one can still use the flac binary to decode flacs to wav and then pipe it to SoX, lame or whatever.
> Apparently this does not work for flac/cuesheets (why?).

>Unfortunately I don't see me compiling SoX with flac support any time soon (absolutely ZERO time for >anything more than a few comments/hints in the forum).
>
>You can replace the bad sox from SSODS with a good one if you can find it (Optware?) or 
>make it (compile it). If you find one, I'll happily add it to SSODS or put it on my page to download for
> others.

Source: http://forums.slimdevices.com/showthread.php?p=390509

Can anyone clarify the point raised in this regard: why SOX is needed for playing flac files, if both SC and Transporter have native flac support? 

Because they need to be transcoded using a 'flac | sox' pipeline in order to extract the necessary set of sample from the source flac file. This has to be done in SC, not the player.

We used to use a 'flac | flac' pipeline but flac will not do resampling and sox will, so we use sox for all FLAC encoding so that we can downsample if needed.

You could create a custom-covert.conf to override the default transcode rule. A suitable entry would be:

flc flc transcode *
	# FT:{START=--skip=%t}U:{END=--until=%v}
	[flac] -dcs $START$ $END$ -- $FILE$ | [flac] -cs --totally-silent --compression-level-0 -
 

Alan, thank you, I'll try it and post results here.

One more question -- why do you need to downsample flac? The only scenario I have in mind is when flac file is 192khz and it has to be transcoded do 96 khz so that Transporter would play it? Or are there other occasions when downsampling/transcoding has to be done?

The Transporter will play 96000 samples/s  (and 88200) but other players can only manage a max sample rate of 48000.

The following details are for QNAP TS-109 II PRO. I'm not a unix pro, so correct me where I go wrong. 

Here's step by step guide of how to enable flac with cue files on QNAP for SC versions over 7.2:

1. Create a text file named "custom-convert.conf" (using notepad on pc or textedit on mac). 
In previous post Alan made a typo (and I gh.. copy-pasted it and spent extra 20 minutes figuring it out), so make sure the file name is "custom-convert.conf" :-)

2. Add followng lines to it and save the file. Make sure the lines are not wrapped

flc flc transcode *
        # FT:{START=--skip=%t}U:{END=--until=%v}
        [flac] -dcs $START$ $END$ -- $FILE$ | [flac] -cs --totally-silent --compression-level-0 -

3. Put this file in "Public" share of your QNAP (via Web File Manager of you QNAP)

4. SSH or Telnet to your Qnap (on PC use putty, on mac use Terminal)

5. It may be that case that you already have custom-convert.conf. If so, back up your existing "custom-convert.conf" by typing the following:
cp /volume1/SqueezeCenter/custom-convert.conf /volume1/SqueezeCenter/custom-convert.backup

6. Now copy the text file you've created to Squeezecenter folder by typing the following:
 
cp /volume1/Public/custom-convert.conf /volume1/SqueezeCenter

7. Restart SqueezeCenter

Now it should work. 

Alan, thank you for help and last question is whether we still need to bother with sox update proposed earlier or this workaround should be sufficient?

Sorry about the typo earlier.

That workaround will work for now, but please be aware that we will probably change most of the FLAC-producing transcoding rules to use sox instead of flac, so it would be good if someone could build a FLAC-enabled sox for that platform at some time.

*** Bug 11179 has been marked as a duplicate of this bug. ***

Closing resolved bugs - if you feel this bug still exists please first re-test
with the latest SW/FW version.  If you are able to reproduce then feel free to
reopen and attach new logs / steps to reproduce.