Last I checked, UniUploader was only a Windows executable. It was partially for this reason that I wrote my own upload script.
Anyway, from what you are saying, it sounds like you are uploading the wrong SavedVariables file; one holding the per-character configuration instead of the "global" (actually account-level) configuration.
Ignoring the funkiness that can occur under Vista / Win7, the right SV file is located, in the same place on all platforms. It is located relative to the directory where World of Warcraft is installed, at
WTF/Account/<accountname>/SavedVariables/CensusPlus.lua
where "<accountname> is the name of your WoW account (
not character).
It sounds like what you are uploading are per-character files, which would be found at
WTF/Account/<accountname>/<realmname>/<charactername>/SavedVariables/CensusPlus.lua
The reason there are both per-character and per-account files for CP is because the (much larger) per-account file holds the census data for
all realms and factions that you scan, while the per-character files hold configuration / preferences for each of those characters, such as whether "verbose" is turned on, whether to auto-scan, etc.
If you
have been sending the larger per-account file, then the problem lies elsewhere.