Ok, I've spent the past 6 hours trying different combinations of things and here is where I am.
I am running the following
Joomla Version 3.3.6 - Beez3 template
VirtueMart 3.0.6
CleanMart 3.1
There appears to be a conflict between VirtueMart 3.0.6 and CleanMart 3.1 that causes the quantity in the Add Cart button to show "Nan" whenever the "+" of "-" are clicked.
You can view the page here:
At this point I've left CleanMart files enabled.
If I disable these 2 CleanMart files:
\templates\beeze3\html\com_virtuemart\productdetails\default.php by renaming it to default.php.f
\templates\beeze3\html\com_virtuemart\sublayouts\addtocart.php by renaming it to addtocart.php.f
Both the "+" and the "-" links do the correct thing when clicked - they increment and decrement the Add to Card button quantity.
Screen shot below with both CleanMart files disabled - showing the quantity at "2" after clicking the "+" sign.
Attachment cart-qty-flex-diabled-both.jpg not found
Screen shot below with addtocart.php enabled - showing "NaN" in the quantity field after clicking the "+" sign.
Attachment cart-qty-flex-diabled-default.jpg not found
Screen shot below with both default.php and addtocart.php enabled - showing "NaN" in the quantity field after clicking the "+" sign.
Attachment cart-qty-flex-enabled.jpg not found
If you would like to debug this on my site send me a PM and I'll setup an FTP account as well as a Joomla Login so you can look into this.