John, On Mavericks I have seen this issue with Safari but worked ok when I used firefox or launched Netrork Connect directly (6-8 months ago). On Yosemite I have not heard of a workaround.
Please note that these OS are not supported by Network Connect. If you have a chance do try the Junos Pulse Client. It is a newer client and will provide a far better expereince on modern operating systems like Yosemite.