After electrophoresis, the alkali in the gels is neutralized by rinsing slides with a suitable buffer.Three washes of trizma buffer for 5 min each are typically used, however, when a high back ground is found during scoring, increased rinsing may be useful in some situations. Acetic acid is used to stabilize the stain,  clear background by releasing over stain from the slides. Acetic acid percolate inside gel through pores and leach out thick background from the slides.

I come from the histotechnical side to answer partly your question with no practical experience in this special assay.

In histotechnics we call this treatment "differentiation" to reduce the amount of staining to the wanted amount. Dyes have some affinity to their substrate influenced by chemical environment. An important factor is the pH and the electrostatical behaviour of dye and substrate in acid or basic solutions. Lowering the pH and bringing in more H+ ions may also lower electrostatical binding. Another way is, that the acid competes for the same binding sites as the dye. Only the binding of high-affinity reaction partners will "survive" and other (unspecific) bindings will break up.

Differentiation is done always with controlling the results in order not to loose the specific staining. So if you have problems, that after the acetic acid rinse your staining is lost, you have to reduce the differentiation step until the "noise-to-signal-ratio" is correct. 

Usually the a weak acid is used for differentiation of hematoxyline stain in cytological preparations.Dilute HCl is often used for this purpose.Here acetic acid is used as a fixative and de-stain the excess non specific stains  as it is done in CB staining of gels.