Sounds to me like you're trying to use the metronome too fast in the beginning. At first start out slow, maybe 60BPM or even less if that is necessary, play one note per beat on one string, then slowly increase it up to where you want to be, maybe 120 BPM or more I dunno? Then lower the speed again down to 60 BPM and then try one note per beat while you are running the scale from low E to high E: E-F-G-A-B-C-D-E-F-G-A-B-C-D-E-F-G and back again, slowly increase your speed up to where you want it to be. Remember if each and every note on every string is not sounding out like it should be then you are going too fast.
After that you can try two beats per note, then three and so on until you can run that scale forwards and backwards without mistake at whatever speed you want it maxed out as. Once you can do this then you can try other scales and patterns one at a time until you feel good enough that you can do anything at any speed. of course I simplified this quite a bit, but I think you get what I mean?
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