Experiencing the same problem with bittorrent after a firmware-upgrade to version 1.60, I finally found a solution that is likely to solve your problems too.
Some time ago a guy named Shonk started a great job by modifying Buffalo's firmware, including version 1.60 which seems to be the last firmware version for the LS-CH1.0TL-V2, because this model is presently to be found under "discontinued products" (yes indeed, this is questionable support). Shonk even modified further versions of the firmware, meant for other models, and tested it for proper operation on a number of devices, including the LS-CHL v2. At the time of writing this reply, he arrived at version 1.64 mod1a.
I installed the last mentioned firmware (with fingers crossed) on my Linkstation, and yes, it turned out to be working like never before! Not only bittorrent is working now as in the old days, but various other features have been added (for instance I can't remember to have seen the SqueezeBox server in previous official firmware), or have a newer version (like TwonkyMedia server). You can read all about this here:
http://forum.buffalo.nas-central.org/viewtopic.php?f=68&t=23603
The download link mentioned on that page didn't work for me, however this one did:
http://download.discountnetz.com/oxygenacht/ls_series-164-mod1a.zip
I would be happy to learn from you whether this turns out to be THE solution. If so, I suggest to erect a statue for Shonk.
Good luck.