There are a number of possible reasons for the differences you are seeing.
Spring honey will generally be lighter depending on the source, fall honey is generally darker.
Also take into consideration straining/filtering methods. Not all are created equal. Some prefer clean honey where some don't mind a lil extra junk (pollen, wax, etc...). The cleaner it is the clearer it is but then again if it has some age to it, of course again, depending on the source it could change from clear to cloudy.
As the bottom stuff crystalizes first, you'll have a separation of the crystals at the bottom and what liquid is on top. This will give you some color change as well.