okay. so this has been happening for a while and I have been ignoring it... it has not gotten any better or worse.
I have an old shoplight fixture that I rescued out of an old barn a while back, it is preheat and takes 2 40 watt T12 lamps.
I am not sure of the brand of the ballast as the paper is gone but I could attach a picture if that would help (it is just a standard preheat ballast for 2 40 watt T12s) It is pretty old because it has the cloth wire...

the Issue I am having is that when it is first turned on in the morning after being off all night (and temperature affects this as well) one of the two lamps blinks like it is EOL for 2-3 minutes until fully heated up. I have tried different starters, different lamps, only running one lamp in the side that blinks, and it still does the same thing. blinks like it is EOL for 2-3 minutes. once it starts to get warmed up it will stay on for a few seconds and then go off and re-strike again. but once it gets warmed up and it stays on then it is fine, you can turn it off for an hour or so and it will come right back on, there is no difference in brightness between the lamp that has the starting issue and the one next to it. I am just wondering what is going on there, as one side is fine and the other one almost always does this. (I did not mention this, because it is preheat and does not make a difference but the fixture is not grounded, which for preheat should be fine right?) 

Is it wired correctly ? Usually on these ballasts, one of the starter loops must go through a starting compensator in the ballast on the lead lamp only to increase the starting current.

I do not have a wiring diagram for the ballast as I have no idea the model or brand as it is gone, and the old cloth wires have all pretty much turned the same colour... I do believe it is wired correctly as I have never changed anything and it did work for a while when I first got it without blinking, but it started after about a month of use and has been doing it for almost a year.

When the lamp in question finally does start up, does it exhibit a shimmering flicker, somewhere between rectifying and normal operation?  The behavior you describe sounds similar to what I've encountered attempting to operate 36W T8s on the lead side of some two-lamp preheat ballasts.  Depending on the starter, the 36W may never light or it may start, shimmer, restart a multiple times over the course of a minute or so, and finally remain lit.  The flicker diminishes as the lamp warms up.  Of course you're using regular 40W lamps.  I wonder if a faulty capacitor could be to blame.

no, it is slightly dimmer once it first stays on, but not hardly noticeable unless you were really staring at it. other than that, it is completely normal when it finally does start. I will say one thing that I failed to mention. once it is warmed up it runs fine and will restart fine if it is only off for about an hour or so, but running new lamps that are supposedly better like an ecolux or an alto lamp, it struggles to run that lamp at all even when warmed up. but running normal lamps it is fine once warmed up. when i first got it it was fine until it started that one day, and it has been over a year, the fixture is pretty much on all day from when i turn it on at about 8 in the morning until i turn it off about 12 at night, and it has not changed in behavior or gotten any better or worse. i guess it could be a capacitor, but it seems like with the heat cycles and such that would have gotten worse by now if it was going to. 

Curious it doesn't flicker.  Being dimmer might be related to the issue, or that could simply be due to the lamp being a bit cooler than it's partner, on account of it lighting later.  I wonder how it'd behave if preheated with a manual switch instead of a starter.

that may be something I try as I have never thought of that and it would be interesting if it would stay lit.

Okay, not that I want to revive something that has been forgotten about, but... I have made a few discoveries after playing around with it. first thing I noticed is my line voltage on the circuit it is running off of is low, I already knew this but kind of just forgot about it... is is anywhere from 116V on a good day to 104V on a bad day. The voltage in the house generally runs about 123 at the panel, so a good bit of voltage drop and most likely heat somewhere... so I will be checking into that, although it has been like that for YEARS. anyway, when connected to a higher voltage it does the same thing, so that does not seem to be affecting it in any way. the second thing I checked was manually preheating it like mentioned above, when doing that it acts like a lamp that is starting to EOL would on a manual preheat circuit... when heated it initially lights up, then after about 1 or 2 seconds it slowly starts to flicker out and die, it will do this as many times as wanted (presumably until the ballast heats up at which point it will stay on, like it does with the standard starter). I wonder how one of those electronic starters would act. probably would be about the same just maybe a bit less sporadic? one more thing I just thought of while writing this is the contacts in the lamp holders. the fixture had been in a damp barn for years before I rescued it. I have had issues with the contacts in the past where I had to wiggle the lamp around to get it to make a connection, could high resistance due to corrosion on the contacts possibly be causing this? i guess it wont hurt anything to try to clean those contacts up either way, it would probably be beneficial. I don't think that will really make much of a difference, but I will clean up the contacts and see, if it makes a difference I will post an update, if no update is posted in like a day or 2 then I guess it is safe to assume that cleaning the contacts made no difference.