Its about the ethics (and the optics) of the matter, Mr. Emanuel

Founded by the late Jack Layton, the Federation of Canadian Municipalities (FCM) describes itself as the national voice of Canadian municipalities.  Its an important organization, working with politicians of different political stripes in Ottawa advocating on behalf of municipalities right across the land. 

As such, the FCM has rules that is asks its board members to comply with.  Specifically, FCM board members are required to (excerpt from the FCM):

ACT WITHOUT POLITICAL PARTISANSHIP –

FCM is a non-partisan organization with an

enviable reputation as the voice of all Canadian
municipalities. It has been successful, in part,
because it places the common interests of all
Canadian municipalities before those of any
political party, whether in power or in opposition.
Protecting this reputation for non-partisanship
is of paramount importance. Board members must
therefore avoid any form of political partisanship
when making decisions on issues brought before
the Board or when speaking on behalf of FCM.

Newmarket's Councillor Chris Emanuel is a member of the board of the FCM (see here: http://www.yorkregion.com/news/article/1352913--newmarket-backs-emanuel-s-return-to-fcm)

Disturbingly,Councillor Emanuel also serves as an executive for this organization too: http://newmarketaurora.ridingassociation.org/pAboutUs

And he says "partisan"-like comments, like this: 

"Just putting his name on the ballot makes everyone proud," campaign volunteer Chris Emanuel said. "Everyone here knows how passionate Kyle is. This is just the beginning. Next time, Newmarket-Aurora is going Liberal." (Newmarket Era, May 2, 2011)

It's hard to square Councillor Emanuel's partisanship against the rules of FCM because the "Act without political partisanship" clause appears so black-and-white.  It comes down to a judgement call about whether this Council member/ FCM Board member/ Newmarket - Aurora Ontario Liberal Party executive member can participate in all of his duties without sliding down the slippery slope that FCM policy had hoped to avoid.   

You don't need an actual criminal conviction (although Councillor Emanuel has one) as proof of Councillor Emanuel's history of questionable decisions such as choosing to participate in partisan politics while simultaneously serving on the FCM board that places him on the wrong side of the spirit of FCM.  Jack Layton wouldn't have approved.