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My question is this:
1. There is only the *one* sub-domain
2. There are clear links/associations between the two sections
3. The two locations will have differing IPs (they have different server needs)
Will inbound links to the sub-domain in this case benefit the main domain?
Myself I see this as a legitimate need that SEs should probably take into account - but it never pays to assume (especially given how sub-domains have been abused in the past).
In this case the sub-domain will certainly be getting more inbound links that the main domain - and it's that main domain which badly needs an improvement to PageRank.