Ok. Alan, we seem to be hitting and missing one another so Ive written up a guide for you to follow. If Im not as clear as I feel I am then feel free to let me know and we can go from there.
I did a bit of investigation and found out that september 6th the wordpress server was buggy - you can read about it HERE
So that may have been your problem. If not try this:

add your template to your bluevoda file
open blueftp
connect
on the left scroll down until you find the file 'wordpress'
double click wordpress
double wp_content
double click template
highlight new template on right
at the top of Blueftp click move to
tick include subdirectories
click ok
your new template will then copy to your ftp
after file has finished copying to the right side
double click both folders on right and on left to open the files
You should see the exact same thing on both sides.
if not...again highlight the missing file on left and copy to the right.
you should see other folders within.
double click those on both sides and check to see if all files have copied.
continue thru each folder until you are sure all files and subdirectories are in fact copied over to ftp area...
if all are the same on both sides your new template should show up on your wordpress blog.