Google has trended towards devaluing links between domains with "Administrative Relationships." It's a good bet that they can figure out you own both domains.
That said, it's only a devaluation. The links still count - just not as much. Think of it more like internal anchor text from your own site. Like Nakul said, since it's only one domain, you're not going to suffer a "link-wheel" scheme penalty or anything similar. It's natural and normal for sister sites to link to one another - even groups of sister sites. But the links likely won't help as much as external links form outside sites.
It's possible that there's 100's or 1000's more we're not seeing, and these are causing either a manual or algorithmic penalty.