1. Yes, it's a problem. Whenever you want to withdraw money from the traditional pre-tax IRA, the default position of the IRS is to tax it all. Your only claim to having a non-taxable basis is your accurate and timely filed form 8606 (or 8606's). There is also a $50 penalty for every form 8606 not filed. Technically, you only need the most recent 8606 when you file a tax return, and that creates a new 8606 that you use the next year. But you should keep them all, so you can prove the history of your taxable basis if audited. You should file amended tax returns to update, correct, or add missing form 8606s. Because each form flows from the previous, you will have to go back to the last fully correct 8606 and work your way forward one year at a time.
2. Your rollover IRA does not contain any after-tax basis from your work plan because the after-tax basis was rolled over to a Roth IRA. They are different and separate.
