Can't Access Site Via FTP

I'm not sure if this is an issue related to my Airport Extreme or my Virgin Superhub...
I have a Superhub that is set to modem mode connected to my AE and there are a couple of websites that I am unable to access via FTP. (I use Transmit as I'm on OSX 10.7.4 and am able to connect to several other websites.) I have only noticed this recently, and can only think it may have been since the 10.7.4 update.
When I am NOT using the AE and the Superhub supplies my wi-fi I CAN connect to these sites. Does anyone know what may be causing the issue?

It can take quite a long time to publish a site. Mine takes more than an hour. And I don't see anything moving in the publishing wheel for about twenty minutes, then slowly the clockwork starts moving. Depending on the size of your site you may have to let it publish (and don't let your mac go to sleep while it is publishing) for more than an hour.

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