I just took time to fill my shop bottles with plastic from a 5 gallon pail. One of the smaller bottles had some product in it yet and when I set it with the others to top it off I noticed some substantial separation in the bottle so I dumped what was in it back into the bucket and got out the 1/2" drill and paint mixer. The pail had some separation in it too so now was a great time to do a healthy re-blend using the power mixer instead of a shake job. In a cold environment the plastic is at its densest and will settle fairly fast and in a more pronounced way. If possible keep your plastic where its warm.
Like your colorants, the bulk plastic needs to be shook up well occasionally whether in a bottle, in a box or in a pail. I do pails and dole out smaller quantities in quart and pint bottles that stay on the work bench in warm weather. I use a $7.00 Menards paint mixer that fits in a 1/2" drill to mix my pail stock and it does a super good job. 3 minutes. Since any form of agitation will put air and bubbles in the raw plastic its a good idea to do this during a down time so those tiny bubbles and air can void themselves. I fill my smaller containers right away after mixing the pail but won't use any from them for a couple days.
Also, I work in an un-heated garage and cold weather can play all kinds of games on the plastic while it gets cooked in the microwave so I store my smaller jugs in the house in a warm area so there is less chance that my little micro-bubble buddies come visit when I do cook up some new plastic.