"What were the problems with SLC 6 launch pad at VAFB?"
The problems ranged from the sublime to the rediculous. At the rediculous end of the scale, there was a serious problem with the quality control on the project: a lot of the welding work was suspect and had to be redone. And this was on a $6Billion project! Also, the site was more windy than the planners had originally realised so that stacking the Shuttle in the open was not an option. As a result they had to build a shuttle assembly building on wheels so that it could be rolled back to launch the Shuttle (at the time it was the largest movable structure ever built). There was also a serious concern after STS-1 that the shape of the surrounding landscape might amplify the acoustic wave caused by the SRB ignition, so they had to redesign the sound suppression system and also remove a hill.
At the more sublime (though potentially more deadly) side there was the problem of hydrogen entrapment in the flame ducts. These were originally built for the hypergolic Titan-2/3 launch vehicle which meant that gas buildup wasn't factored into their design. As I'm sure you know, H2 that boils off from the ET during the launch countdown is vented through the SSMEs. It was recognised that there was potential for this hydrogen to build up in the ducts and it was widely believed that it would explode on ignition of the SSMEs which would damage or destroy the vehicle. There was an ongoing project to design a system to either vent, neutralize or burn off this H2 prior to engine start.
While the problems with the site were numerous, they were just about solved when Challenger exploded. Up to that point the VAFB site had cost about $6-7Billion dollars (between MOL and STS), I've seen it claimed that it would have cost less than $500Million to fix the problems. However, given the ongoing problems with developing the filament-wound booster casings (which many believed would explode on ignition) and continued weight growth of the KH-11 satellites, the DoD was already out of love with the Shuttle, so they shut down the project.
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A far more detailed summary of the SLC 6 boondoggle can be found here: http://www.fas.org/spp/military/program/launch/sts_slc-6.htm
Actually, SLC-6 cost more than what the FAS link alluded to. It was originally part of the MOL program (along with the "Blue Cube"), which was canceled in the late 60s. There were folks who seriously believed the site was cursed. In fact, there was an article a few years back in "Florida Today" called "The Curse of SLC-6".
AFAIK, There was only one successful payload ever launched out of SLC-6.