OK, your file does not actually import into LOR S3 correctly. Unit IDs are limited to 1 through 240 (01 to F0). When using 16 circuits per unit id, you are limited to 3840 channels per network. You need 16x100x3=4800 to represent you configuration. You can see the error in LOR if you open the channel configuration grid and scroll down to S14-P1-R. You'll notice there that the network is empty. That is because you generated an invalid unit id (241-255/F1-FF). You also generate unit ids above 255, which LOR just chops off the higher order bits. So on channel S15-P28-R, which is listed in the file as unit 264, it shows as unit id 08 (264 modulo 256) in LOR.
To fix it, I think you are going to need to generate the network attribute in your lms file. So S15-P28-R should be:
unit="8" circuit="82" network="1"
Hope that helps,
Matt