This is not the only file I had these same issue with but since I just made it I knew all the version numbers etc. several files start stuttering and I have to rewind or fast forward a bit and it plays fine. With this file it will happen in the same place every time. Plus the fast forward and rewind are very messed up. Sometimes I can fast forward and I watch it to the point I want and when I hit play it goes back to where I started.

This is from The Run Down, when the jeep falls off the cliff into the water after the actors. It would start stuttering there every time.

I use ISO files and maybe that is an issue, I have not had time to rip the m2ts out and test it yet. I tried both the normal way I make the ISO files outlined below and I also tried ClownBD v.59. If it was only this file I would just move on but it is not.

Firmware 1.02.07
HDMI to Onkyo 605
WD 1TB HD

To make the ISO:
AnyDVDHD 6.5.5.9
tsmuxer 1.10.6 (used on the above movie anyway)
select only the movie and 1 audio stream no subs
downconvert HD audio to core
mux to BD structure
Create ISO with IMGBurn

If it is a branching disk I use ClownBD since it uses eac3to to demux.

Here is the mediainfo on the m2ts:
Video
ID : 4113 (0x1011)
Menu ID : 1 (0x1)
Format : VC-1
Format profile : AP@L3
Duration : 1h 44mn
Bit rate : 17.3 Mbps
Width : 1 920 pixels
Height : 1 080 pixels
Display aspect ratio : 16/9
Frame rate : 23.976 fps
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.348
Stream size : 12.6 GiB (88%)

Audio
ID : 4352 (0x1100)
Menu ID : 1 (0x1)
Format : DTS
Format/Info : Digital Theater Systems
Duration : 1h 44mn
Bit rate mode : Constant
Bit rate : 1 510 Kbps
Channel(s) : 6 channels
Channel positions : Front: L C R, Surround: L R, LFE
Sampling rate : 48.0 KHz
Resolution : 24 bits
Stream size : 1.10 GiB (8%)
Language : English

"Do you see any reason the WD-TV should not play this"

No. :)

I haven't tried iso for BDs, I only have used basically the same system, but using MkvMerge to remux the audio and video into a single .m2ts, instead of muxing it back into a BD structure.

How are you stripping the audio to the core? Eac3to?

I use tsmuxer most of the time I only use eac3to (using clownbd as front end) when it is a branching disk because I have had issues with tsmuxer on branching titles.