I don't know how you got that in v2. It has always been TB's way to not quote blank lines, since v1 and on into v3. The only way to get blank lines to be quoted is to use the "Paste as quote" function, having copied your quotable text into the keyboard.
Yeah, since then the author of the previously mentionand quick template has told me the soltuion for The Bat! v3.x:
In Account|Properties|Tempates|Reply, in the template, the %Quotes should be replaced with %QuoteEmptyLines%Quotes. (It's pretty simple, just it seems to me that the QuoteEmptyLines macro is not mentioned in the help.)