While doing gel PAGE, my molecular weight marker did not stack. It started resolving in stacking gel itself. I have checked pH of all buffers, they wr 5ne.
If you are making the separation gels yourself, have you checked the stock % of acrylamide you are using? Sometimes the stock solutions you buy commercially are 40% and not 30%. Perhaps this could be issue, with the stacking gel having a % too high through a miscalculation?
Again if you are making the gels yourself, you are using the correct buffer chemistry in the gels themselves? That is either Bis-Tris or Tris Glycine? Perhaps your running buffer is not compatible with your gel buffer?