Got this figured out w/ Robert's help - (thanks robert!)
For any Mac users on Coda/Transmit note the following:
The upgrade process with CPV Lab is simple, HOWEVER, the upgrade folders do not contain all the same files as the installation downloads.
What this means:
both the db_params.php and license.php files which ARE contained in the original purchased download (whenever you do this, no matter what version, at least currently) are are, per install instructions, required to be chmodded (as you all know).
However, the upgrade within /lib/ there is NO db_params.php file, and within /license/ no license.php file.
The default behavior of many ftp clients (filezilla on pc's for instance) is that when you select 'overwrite' within a sub folder (ie /lib/ or /license/) it doesn't overwrite any files that aren't present - thus your db_params.php and license.php files remain untouched.
There is good reason for CPV Lab to do it this way due to their requirement of changing file persmissions - it doesn't make you remember to do this upon every upgrade.
HOWEVER
On Panic (Coda/Transmit) programs the default behavior upon 'replace all' is to functionally delete sub folders (ie /lib/ and /license/ )and re-upload all the contents of these new folders.
You can see the problem here- we've lost two of our critical files - license.php and db_params.php.
Prosper functioned differently in that any needed files were contained within subsequent releases, so for those of you coming from Prosper (like me) TAKE NOTE OF THIS.
The solution?
Really simple, manually go into the 8 or 10 subfolders and open these on your desktop downloaded 'upgrade' version and on your server, and copy the FILES only into each subfolder. Once done upload all the FILES only (not folders) from your CPV Lab upgrade download on your desktop to your server.
This will ensure within your /lib/ and /license/ folders your original, and correctly chmod'd license.php and db_params.php files are still there, and when you then run the upgrade script to move to a new version you'll have no issues.
I'm sure most people aren't as dumb as I am and this is obvious, however perhaps this can help one of you who had the same confusion I did.
Cheers