Diesel Bombers - Weird Starting Issues

Tempatures have been dropping lately so earlier in the week I thought the slower cranking was due to the cold. Two nights ago, when I went to leave work, I turned the key on, all the normal dash lights came on, went off, and then the check engine light and the low fuel light came back on and started flashing along with a weird click, click, click coming from under the dash and it would not crank over. I turned the key off, waited a bit, turned it back on and the instant I saw the check engine light go off the first time as normal I cranked it and it fired right off with no hesitation. Drove on home stopping at Safeway on the way and it re-started there just fine as well.
Then yesterday morning it was slow again but cranked over and off towork we went.
But then last night when I went to leave to come home again, dash lights came on and went off like norrmal, but the check engine and low fuel ight once again came on and stayed on, no flash, no crank nada. Several tries-no change.
I opened the door to see if I could hear anything happening outside and the dome light in the roof started flashing like a strobe light till I closed the door, I thought, what is going on here. Went back in the shop and grabbed battery and cables. I connected and as soon as I could get back in the cab, it fired right off with no hesitation at all. Drained batterys at this point I would think would still crank slow.
I'm flusterd, would dying batteries cause this strobelight and what sounds like a clicking relay sound to occur, and after starting and driving, it does not show excessive charging on the volt meter, that shows normal as well :argh: