I'm not exactly sure what you're doing after piling the glitter onto the still-tacky resin surface, but there are a few things I think could be problems:
...when mixing parts A and B of clear resin, it's not necessary to stir *slowly* or for 5 minutes....it's usually stirring fairly rapidly (although without raising the stirrer into the air each time which will whip extra air into the resin) and for 2 minutes each in 2 sequential containers
...resin is usually poured into molds, or otherwise used, right after mixing not after waiting (if you're doing that to prevent natural bubbles, there are other ways to prevent and get rid of them)
...you said: ". . .letting them (mixed A + B) sit for another five minutes.
>> Next, I pour them into the molds (Padico brand) and waited until the resin mixture is slightly tacky before putting my *resin* in.<< I then waited for another 30-45 min for the mixture to turn very tacky (before adding glitter). . . " I don't understand the part between the brackets >> <<. What exactly did you pour into the molds if it wasn't the mixed resin??
...you then said that after the 30-45 minutes of sitting --the 2nd time the mixed resin had sat-- you dumped in glitter... was that the last thing you did? or did you then cover the glitter with more resin as would be normal?
(and if you didn't add more resin, the "very tacky" resin you dumped the glitter on probably wasn't liquid enough or still adhesive enough to grab onto much of the glitter... and if you did add another layer of clear resin on top of the glitter, the poured resin would have disturbed the heavy layer of glitter you used and created uneven areas)
Often what's done in situations where a *layer* of glitter is wanted in a casting, the glitter is mixed into a small amount of clear resin separately then added as a separate layer somewhere in the casting once the previous layer has firmed up a bit (or that glitter-mixed-into-resin is just used as the last layer which will end up being the back side of the casting).
Or often glitter is just mixed into all of the resin, or most all, then poured (and perhaps something is added on top of that when tacky and a final thin layer of clear resin is added to create an even surface, etc).
But rarely, something like what you did is created though this one uses clunky flake glitter and looks different.**
I don't know why some of your glitter got "darker" though the clumpiness would be explained by the thick layer of glitter you used, and/or not mixing the glitter into resin separately if you want it to be only a layer of glitter. The darkness may only be an effect of the clumpiness (shadows, etc), for example.
If you want to read a lot about using various kinds of art/craft resins (including the "tweaked" epoxy resin with the brand name Easy Cast, which has a few problems of its own), check out some of my previous answers here on resins:
https://answersrip.com/question/index?qid=20140118071238AAOocua
https://www.google.com/search?q=how+to+use+glitter+in+resin+in+molds
https://www.google.com/images?q=how+to+use+glitter+in+resin+in+molds
** http://resincrafts.blogspot.com/2012/07/glittered-roses.html
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