This seems to be an area of great confusion. I can only provide the information that I have found. The Revenue Procedure cited in the attachment Revenue Procedure 2013 - 12 is the latest version of EPCRS, in that document the IRS states that in matters involving excise tax if the revenue procedure does not specifically address the situation, then EPCRS cannot be used. The failure to deposit salary deferrals and loan payments is a violation of IRC Section 4975. The lending of money between the plan and the employer is a prohibited transaction loan. This prohibited transaction can only be corrected by repayment of the amount involved and the filing and payment of excise tax on the form 5330. The IRS issued Revenue Ruling 2006 -38 to deal specifically with the issue of late deposits and their correction. In that Revenue Ruling the IRS states that using the Section 6621(a)(2) rate is appropriate to calculate the amount involved. The Department of Labor calculator uses the cited code section for it's calculations.
Based upon everything that I have been able to find, the use of the DOL calculator seems appropriate. A recent review of the 401(k) Fix-It guide indicates that EPCRS correction procedures would only be appropriate if your plan document contains a provision that specifically states the number of days by which the deposit must be made. In that case the violation is a failure to follow the plan document and the lost earnings section of the procedure would be applicable.