A couple of months ago, we converted my wife's traditional IRA to a Roth IRA. We are planning on adding another $2000 as this year's contribution. However, a customer service representative from Vanguard, (where the account is), told us that we should open a separate account for this contribution. She was very adamant against commingling the assets, but, unfortunately, she wasn't able to explain why.

Since I won't be 59 1/2 for about 38 more years and the amount in my current IRA is pretty small, I had the same question. Here is the reply I received from the Vanguard rep. as to why they encourage separate accounts:

There is no difference in tax treatment if the conversion assets are held for five years. However, if you choose to mix contributory and converted
assets you will have to keep an exact track of what assets you have contributed, what assets you have converted, and the respective earnings of each. The tax treatment of conversion assets and of contributory assets prior to the five year threshold differ. Vanguard urges are clients to maintain separate accounts to simplify record keeping. However, the differences in tax treatment end after the initial five year period. If you do not foresee a withdrawal within the first five years, you may want to combine the two, and avoid the possibility of higher fees.