QuickTime X not exporting 1080p and 720p correctly?

I've attempted to convert from a variety of different formats to 1080p and 720p, they produce a file with a blank (black screen) and no audio, 420p seems to export perfectly though.

It would help to know what compression format/file container you are using for a source, what application you are using to make the conversion, and what compression formats/file containers you are targeting. My guess is that you are attempting to use the QT X.1 app which many users report is not stable and subject to numerous problems under Lion OS. My advice would be to use a different application like GarageBand, QT 7 Pro, MPEG Streamclip, HandBrake, etc. until Apple gets some of these problems worked out.

I'm using QuickTime X.1 on Mac OS X Lion. I don't have QuickTime 7 as there is no available download for Lion and I would prefer to keep to QuickTime anyway.

QT 7.6.6 Player app for Snow Leopard and Lion This link provides instructions for installing QT 7 on Snow leopard and Lion systems, as well as, a link to the QT 7.6.6 Player download page. It also contains instructions for keying QT 7 for "Pro" use if you decide to go that route. (MPEG Streamclip is, of course, free and GarageBand is already installed on your system.) If you really plan to stick with the QT X.1 Player and its presets, then you might try re-wrapping the file data to a different file container. Some users inidicate this sometimes makes non-playing files playable. I find it much more productive to use QT 7 Pro as my primary player for general viewing, making quick file examinations, and performing "quickie edits/conversions using both presets and user selectable setting work flows.

I've used a number of different formats as the source (.mkv (H.264 & AC3) & .mp4 (H.264 & AAC)) are the most common.

I tend to stick to H.264/AAC/AC3/Chapter content in M4V containers for general compatibility with mobile/TV/computer use and Internet streaming purposes as I am not having problems with this data format/container combination on my system. While I generally prefer using M2TS files for converting 1080p content to 720p M4V (H.264/AAC/AC3/Chapter) files, the MKV container is my secondary choice. In both cases I use HandBrake as the primary converter.

I'm going to try QuickTime 7 Pro, is it possible to define the 'exact' same presets into QuickTime 7 that are in QuickTime X?

Impossible to say. While I assume the device presets would be the same, QT 7 Pro does not include progressive H.264 presets as such. At the very least, you would have to use the movie to QT (MOV) export option to enter your manual setting if you know them all (which I don't). I personally would be more likely to use the x264 option settions for interlaced to progressive target content in QT 7 Pro or the Compressor app (unles converting from BD sourced progressive content for which I prefer HandBrake).