i had the same issue. After trying to find what was going on, I tried to look into where Cydia installed Summerboard and Customize themes were being put. It was no surprise that I found a Customize folder in /var/root/Library and /var/mobile/Library and that is probably why my Cydia installed Customize sounds were not showing in my Customize GUI.
I think (my theory only) that Customize looks for its stuff in /var/root/Library. On the other hand, Cydia installed stuff saves directly to /var/mobile/Library and thus its not being seen by the Customize app. I moved the stuff from the "mobile" to the "root" and it solved my problem.
Try to SSH into your iPhone and check if the Summerboard themes you installed from Cydia are in /var/root/Library/Summerboard/Themes (the opposite of my Customize issue, Summerboard seems to detect themes placed in /var/mobile/Library/Summerboard/Themes)
If this is the case, simply transfer the Summerboard themes from "root" to "mobile" and you should be set.
Or you could also create a symlink from "/var/root/Library/Summerboard/Themes" to "/var/mobile/Library/Summerboard/Themes"
Hope you get it sorted out
