I don't understand why the existing plan assets weren't invested for two months, though. Were they sitting in a non-interest bearing account all that time waiting to be transferred? If so, why? In any event, it would seem the plan fiduciaries should restore lost earnings to the plan. It seems to be a 404 issue - general breach of fiduciary duty. No prohibited transaction with respect to these funds appears to exist, based on the info you provided.
With regard to EE deferrals, per DOL regs, deferrals must be deposited as soon as administratively feasible, but no later than 15 business days following the close of the month during with the contributions were deducted from employees' pay.
In some cases, the DOL has held sponsors to a stricter standard when the sponsor has demonstrated, in the past, its ability to deposit contributions faster. For example, if the sponsor has a history of depositing employee contributions two weeks from the date of withholding, but then for whatever reason starts depositing them later, but still within the deadline imposed the regulation, the DOL has deemed those contributions to be "late" and characterized the resulting extension of credit as a prohibited transactions.
Many sponsors and TPAs think this DOL policy is unreasonable. I happen to agree, unless there's some indication that the sponsor is intentionally taking advantage of the plan participants.
Bottom line -- if there are legitimate business reasons for having deposited the contributions later than usual, yet the deposit is still made within ultimate deadline and the amount of lost interest is relatively immaterial, it is extremely unlikely that the DOL or the IRS is going to pursue any sort of action or excise tax assessment. I guess it could happen, theoretically, but I've never seen it.
The excise tax is the 15% times the amount of interest lost -- NOT the total amount of the late contribution. Because of this, and unless the late contributions were very large and very late, the amount of the excise tax is usually de minimis (pennies, a few dollars).
In terms of whether it's worthwhile to utilize the DOL's VFC program, I'd encourage you take a look at these two articles:
Is the DOL's voluntary correction program more trouble than it's worth? (Plan Sponsor Magazine, July/August 2000; free registration required)
http://www.plansponsor.com/archives/test/0...psjul00_084.asp?
Friend or Foe? The Pros and Cons of the New Department of Labor Voluntary Fiduciary Correction Program by Marcia S. Wagner, Esq.and Deanna H. Niņo, Esq. (former PWBA investigator, Boston Regional Office). A discussion of the pros and cons of the VFC Program, and the circumstances under which participation in the program might not be desirable.
http://www.erisa-lawyers.com/pages/misc/fr...friend_foe.html