I compiled the instructions you've likely followed. The link in your above post points to the tree changing in a Qnap, so I guess you followed the ones here
. I've used them to install 6.0.34 in a couple DNS323's (for friends) and a few others have also successfully followed them. One person had all sorts problems and it took us ages to get to the bottom of it. It turned out that he was installing it using a Windows 7 PC and for some odd reason, it wasn't installing all the files via the Twonky telnet installation script (and Twonky simply wasn't starting). Most odd, and I can only assume it was some security feature in W7 that was causing the problem, but when he tried it on a borrowed XP laptop, it sailed on and Twonky started as expected.
The only critical bit about the installation is to untick the start Twonky checkbox that appears in the installation utility. If you forget to untick that, it will start Twonky and fill up the root. By unticking it, it prevents Twonky starting, and after the NAS reboots, it picks up the symlinks and then starts Twonky with everything going where it should be. Could it just be that tickbox issue?
It looks like we were both typing at exactly the same time!