MR11 can be used to clear only GR & IR differences that happen due to quantity mismatch between GR & IR. MR11 will not clear small differences which you have referred as this might have caused due to exchange rate differences or multiple account assignments etc.
The only way to clear these small differences is to post a manual adjustment posting to the GR-IR account. Such activities are part of normal year end closure activities as GR-IR accounts are normally set-up as not allowed for manual postings. So a G/L account set-up change is required and this is reason for such clean-up being part of year end activity.
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