I have experienced this issue and tried using float and currency precision to overcome it but that only achieved so much since paid amount as you rightly put it ignores the rounded total.
Probably a sales setting to allow sales payment against rounded total is needed for this to work. However I do not know the full impact of that approach in GL or elsewhere
hey @mdwala,
What version of ERPNext are you on? The version 10 (Released 6 days ago) has a fix for this. (Again, You guys are awesome - Team ERPNext).
Please, update to version 10 and have fun using ERPNext…
BTW Happy New Year!!!