Monitor orgs - false positives in Clean Rules
It would appear that in the default 64 comparison set when using Monitor Changes, that SFDC may be returning fieldmappings in non-deterministic order when custom cleanrules are in effect as when Day n-1 org is compared against Day n org, the same cleanrule's fieldmappings are displaced some number of lines away causing a false positive. The obvious workaround is to remove Cleanrules from the metadata to compare but this means one can't detect true variances anymore.
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Phil Spenceley
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Another way would be to apply an XML sort to the metadata so the sequence was deterministic, allowing the comparison to detect true variances.