I suspect that re-packaging the counters into sims3packs wouldn't help, though I could be wrong. However, you should be able to just CASt them or drag the design of the other pieces over them to fix them... it's a workaround rather than a solution, of course.
"On the page, punctuation performs its grammatical function, but in the mind of the reader it does more than that. It tells the reader how to hum the tune." - Lynn Truss, Eats, Shoots and Leaves
The OP is describing what happens when you turn a sims3pack counter into a package file, most likely the case. See if the creator offers a sims3pack version, or make one yourself using TSRW, then install a-la launcher.
They are actually Sims Store content. My brother bought them and then put them all as a bundle into a .package file so I could also have them for my sims and there was so much stuff I didn't want the individual .sims3pack.
My brother experiences the same problems though and he downloaded straight from the store. He's raised the issue with EA but naturally they sent him to the forum and he's had no help.
I think I will just have to use different counters!!