Okay so I figured out how to do the list command on flac files using metaflac and got a report on various versions of the the sample file I've been using.
The first thing I noticed is that none of the files I encoded with ECDDA actually HAVE a seektable! I'm not sure what this means or how significant it is, but given that it is apparently important for seeking (logical assumption I'm trying) maybe this is an important discovery? In light of this the fact that my ECDDA encoded files are LARGER is even more confusing; there is a great deal more metadata in the file encoded with flac.exe, yet its 700k smaller...?
On a sidenote, assuming I need a seektable for all my files is there a way to batch edit 88gb worth of FLAC files automatically?

For reference, below are the list results I got running metaflac against various versions of the file. The first is the originally encoded FLAC file from my archive (encoded with ECDDA). The second is a decode/reencode using flac.exe. The third is a decode/reencode using ECDDA. Note that the only difference between the two ECDDA versions (both of which lack a seektable) is the field "length:" in METADADA #1. For the original its 211, for the reencode its 212.
I'd appreciate any thoughts ya'll have on this post.
Thanks,
rt
p.s. sorry for the number and length of posts, kind of rambling along through this analysis
C:\Program Files\FLAC>metaflac --list DustBowl_original.flac
METADATA block #0
type: 0 (STREAMINFO)
is last: false
length: 34
minumum blocksize: 1152 samples
maximum blocksize: 1152 samples
minimum framesize: 499 bytes
maximum framesize: 3202 bytes
sample_rate: 44100 Hz
channels: 2
bits-per-sample: 16
total samples: 11140836
MD5 signature: b9f374ad94e4dd5aef72b8cf514eb8d7
METADATA block #1
type: 4 (VORBIS_COMMENT)
is last: true
length: 212
vendor string: reference libFLAC 1.1.0 20030126
comments: 7
comment[0]: TITLE=Dust Bowl
comment[1]: TRACKNUMBER=8
comment[2]: ARTIST=10,000 Maniacs
comment[3]: ALBUM=Blind Man's Zoo
comment[4]: DATE=1989
comment[5]: GENRE=Folk
comment[6]: ENCODER=Easy CD-DA Extractor (http://www.poikosoft.com)
C:\Program Files\FLAC>metaflac --list Dustbowl_flacexe.flac
METADATA block #0
type: 0 (STREAMINFO)
is last: false
length: 34
minumum blocksize: 4608 samples
maximum blocksize: 4608 samples
minimum framesize: 1955 bytes
maximum framesize: 12392 bytes
sample_rate: 44100 Hz
channels: 2
bits-per-sample: 16
total samples: 11140836
MD5 signature: b9f374ad94e4dd5aef72b8cf514eb8d7
METADATA block #1
type: 3 (SEEKTABLE)
is last: false
length: 450
seek points: 25
point 0: sample_number=0, stream_offset=0, frame_samples=0
point 1: sample_number=442368, stream_offset=0, frame_samples=696466
point 2: sample_number=889344, stream_offset=0, frame_samples=1521283
point 3: sample_number=1336320, stream_offset=0, frame_samples=2371862
point 4: sample_number=1778688, stream_offset=0, frame_samples=3336073
point 5: sample_number=2225664, stream_offset=0, frame_samples=4239085
point 6: sample_number=2672640, stream_offset=0, frame_samples=5147528
point 7: sample_number=3115008, stream_offset=0, frame_samples=5980445
point 8: sample_number=3561984, stream_offset=0, frame_samples=6846865
point 9: sample_number=4008960, stream_offset=0, frame_samples=7749251
point 10: sample_number=4455936, stream_offset=0, frame_samples=8711213
point 11: sample_number=4898304, stream_offset=0, frame_samples=9607825
point 12: sample_number=5345280, stream_offset=0, frame_samples=10497351
point 13: sample_number=5792256, stream_offset=0, frame_samples=11423757
point 14: sample_number=6234624, stream_offset=0, frame_samples=12389569
point 15: sample_number=6681600, stream_offset=0, frame_samples=13257546
point 16: sample_number=7128576, stream_offset=0, frame_samples=14084905
point 17: sample_number=7575552, stream_offset=0, frame_samples=14976293
point 18: sample_number=8017920, stream_offset=0, frame_samples=15911096
point 19: sample_number=8464896, stream_offset=0, frame_samples=16862879
point 20: sample_number=8911872, stream_offset=0, frame_samples=17740812
point 21: sample_number=9354240, stream_offset=0, frame_samples=18621421
point 22: sample_number=9801216, stream_offset=0, frame_samples=19609638
point 23: sample_number=10248192, stream_offset=0, frame_samples=20619135
point 24: sample_number=10695168, stream_offset=0, frame_samples=21418566
METADATA block #2
type: 4 (VORBIS_COMMENT)
is last: false
length: 135
vendor string: reference libFLAC 1.1.0 20030126
comments: 5
comment[0]: TITLE=Dust Bowl
comment[1]: ARTIST=10,000 Maniacs
comment[2]: ALBUM=Blind Man's Zoo
comment[3]: DATE=1989
comment[4]: GENRE=Folk
METADATA block #3
type: 1 (PADDING)
is last: true
length: 4001
C:\Program Files\FLAC>metaflac --list DustBowl_ecdda.flac
METADATA block #0
type: 0 (STREAMINFO)
is last: false
length: 34
minumum blocksize: 1152 samples
maximum blocksize: 1152 samples
minimum framesize: 499 bytes
maximum framesize: 3202 bytes
sample_rate: 44100 Hz
channels: 2
bits-per-sample: 16
total samples: 11140836
MD5 signature: b9f374ad94e4dd5aef72b8cf514eb8d7
METADATA block #1
type: 4 (VORBIS_COMMENT)
is last: true
length: 211
vendor string: reference libFLAC 1.1.0 20030126
comments: 7
comment[0]: TITLE=Dust Bowl
comment[1]: TRACKNUMBER=8
comment[2]: ARTIST=10,000 Maniacs
comment[3]: ALBUM=Blind Man's Zoo
comment[4]: DATE=1989
comment[5]: GENRE=Folk
comment[6]: ENCODER=Easy CD-DA Extractor (http://www.poikosoft.com)