|MadSci Network: Biochemistry|
There are a number of things to try... one thought I have is that you might be allowing the stacking gel to polymerize too long. Perhaps the first thing is to allow it to polymerize for less time. 30 to 45 minutes is typically plenty of time. If that time doesn't work then you might even want to try 20 minutes.
Another option is whether you are polymerizing under a blowing air duct. This would dry out the gel while it is polymerizing (and also cause the gel to set strangely, giving a weird shape when you run your samples). Also, is the room you are in unusually warm or cold? That can also affect things.
If you are using butanol to overlay the resolving gel while it polymerizes, make sure it is rinsed out thoroughly before pouring the stacking gel. If there is residual alcohol it might be having a strange effect on your stacking gel. Alternately, overlay the resolving gel with water instead, and then just pour it away before pouring the stacking gel.
Make sure your APS and TEMED are not old. As a last resort you can try a different stacking gel protocol (i.e. different ingredients), but if you're using a standard protocol that is unlikely to be the problem.
I hope some of these options are helpful to you!
Try the links in the MadSci Library for more information on Biochemistry.