aiman,
The audyssey is trying to do that by indicating that the accoustic distance of the sub is more than the actual physical distance. It is trying to compensate for that by adding distance thus indirectly adding a delay of when the bass information reaches your ears. As such, you do not need to re-run, maybe you can try some other placement and re-run to see if it improves.

For the front speakers the distances shd be fairly close to the actual distance. That is important. If Audyssey is not getting the front distances correct, then you have something blocking the path of the sound between your 1st mic placement and the speakers.

Don't worry abt the sub distances too much as it indicating some room issues. Audyssey is taking care of it.

Refer this to do proper calibration with odisi. Really helps with the sub.
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Checked the levels again last night. After running Audyssey, all the speakers are at 73 dB, with the sub at ~75 dB. After that, I add +2 dB more for the sub.

No Audyssey to run. Only to rely on my good old SPL meter 

I read somewhere long time ago, that the .1 LFE channel are always recorded at -10 dB lower to allow extra headroom to the whole mix. However, the DTS/Dolby decoders in the receivers automatically add 10 dB to balance the level. So in the end the SPL meter must read at the same level for all channels including the LFE. Any thoughts?