If there's only one SPD... is it written as a single employer plan? Who is the listed employer whose employees are covered? Sounds like what's happening in practice might not be jiving with the SPD. I agree with Luke that the incomprehensible nature of the SPD could present a problem, keeping in mind that the SPD must be written in a manner calculated to be understood by the average plan participant. I'd consider running through an SPD checklist that includes the relevant applicable regs (e.g., 29 C.F.R. § 2520.102-3, etc.).
I also agree with Peter in that you'd want to look into whether the plans are all ERISA-governed. Even if the employer(s) say that they're not, I'd want to look into it myself. Sounds like you have a written document at the very least. Depending on what Circuit you're in, I'd probably run a quick Dillingham or related test. In particular, look out for an ongoing administrative scheme and the source of financing. Double check if the plans fall into a VB safe harbor.
The compliance risk may be evident, but the litigation risk should also be noted. A source of concern could be the disclosures of the SPD to the participants.
A separate concern could be the Form 5500 filings and the SARs. Are they potentially not filing/disclosing for a plan that they think is not ERISA-governed but is in fact ERISA-governed? Are they filing/disclosing properly as a legitimate controlled group or should each employer file/disclose separately?
Just some thoughts. Good catch!