We do not work with Na, but have experienced similar problems with Zn and Cr, so the solution might be useful for you case.
Zn - we found that Zn is leached from some polymers by acid. Mostly from rubber and PVC parts of the standard storage containers. The effect was stronger at high dilutions (0.1-2 ppm of Zn); As a hypothesis: in your case, acid may extract Na from glass containers.
Cr - Recovery was different for samples with Cr(+3) and Cr (+6). To resolve, we prepared two solutions of identical concentrations, one with Cr(+3) and another with Cr(+6). The flame conditions were tuned to get identical signal for both forms of Cr. In application to your project, you may want to see if signal of Na in Acid is the same as Na in water. If they are different and this is not due to contamination, try to adjust the flame.
If none of above helps, you will need to prepare the sample and standard in identical matrix.
Hope this helps