You haven't told us specifically how you are doing this, so I can only make general statements.
You're not going to be able to pinpoint the exact value of jewelry by the markings. About the only way to find out how much gold to expect is to melt, sample, and assay the gold before refining.
Are you inquarting or, are you dissolving the karat gold directly? If the latter, you are likely to have more gold in the residues. Also, if you are running small amounts, the percentage of gold hung up in the filters, etc., is more likely to be higher than it would be with larger amounts.
After precipitating and separating the gold from the solution, there can be a small quantity of very finely divided gold still suspended in the solution. If you let the solution settle for a few days, you will often find a thin layer of gold powder settled on the bottom of the container.
You could lose gold from the solution if you allow the dissolving action to be too vigorous or if you boil the solution. Are there any purple stains around your work area?
If you keep (and burn) all the papers, test all solutions, and if your lab techniques are solid, you should be getting essentially 100%.
I eventually get it out after a few weeks in solution
Can you explain what you mean by this statement? Does that mean that you dissolve the gold and then wait a few weeks to precipitate all of it or does it mean that you precipitate and separate the gold and then, a few weeks later, you get the rest of it from the solution?