Filtering imputed GWAS SNPs based on a MAF difference of 10%
I cannot think of any principled rationale for choosing this filtering strategy. 

However, I am going to take a guess that this filtering strategy is supposed to filter out SNPs for which imputation did not work well?  In that case the appropriate statistic to filter on is the INFO score as described here.

You might consider picking a higher threshold than 0.4 if you feel that you aren't filtering out enough variants.