Well you can't just source a company's standings, but I can show you what I mean.
A second party company by definition is (as stated by wikipedia):
That means Nintendo would either have to own a part or in full skip ltd. OR have payed them/funded their game to make it exclusive to their consoles (like Nintendo and platinum for Wonderful 101 and Bayonetta 2).
Skip ltd. is not owned by Nintendo, only having a close relationship to them letting them publish all their games but one by choice, not because they were commissioned by Nintendo to make exclusive games for them. (Companies owned by Nintendo are 1-up studios, creatures inc, monolith soft, Nd cube, and Retro studios.)
http://en.wikipedia.org/wiki/Nintendo_of_Japan
However it lists partners which it mistakenly calls second party development firms which includes atlus, sega, square enix, skip ltd. etc. but are not exclusively second party. Yes they have exclusives, but that does not mean they are strictly 2nd party (or cooking mama and the ace attorney series would be in the same grey zone. The only difference is skip is much much closer to Nintendo of Japan.)
But you have a point. If Nintendo classifies chibi robo as their own, then they view skip ltd. as a loyal company to them.