It looks like this is not possible.
The viewer doesn’t behave very nicely with a transparent
background due to some bugs in Flash Player, which means you may not
be very happy with the results.
I wouldn’t recommend doing this if it’s for some serious business, but
if it’s just your personal website or something, then I guess it’s
okay.
Source: https://groups.google.com/forum/?fromgroups=#!topic/issuu-platform/nbVcSzxUZC4
Unfortunately this is due to a limitation in Adobe Flash Player. It
doesn’t play nicely with Issuu when we use a transparent background.
We might be able to work our way around this in the future, but as of
now it’s hard to say.
Source: https://groups.google.com/d/msg/issuu-platform/jNwGg9BLTH4/lylgM2jrcikJ
