According to this and other sources:

According to NASA engineer Greg Katnik, the 1997 tile incident was traced to an important change in the shuttle foam. Prior to 1997, the foam was made using Freon. After Freon was banned because of concerns about its potential to deplete the ozone layer, NASA switched to a new kind of "environmentally safe" foam. A 1997 report by Katnik described photographs that showed massive amounts of foam missing from the fuel tank after launch. If the new foam helped protect the ozone layer, its impact would be so tiny as to be immeasurable.

If this is true, then going back to the original foam formula might reduce the problem.

Here's a Google search on +Shuttle +foam +freon. It returns 4,450 hits. A narrowed search turned up this article on NASA's website about the 1997 STS-87 mission:

Immediately after the Columbia rolled to a stop, the inspection crews began the process of the post flight inspection. As soon as the orbiter was approached, light spots in the tiles were observed indicating that there had been significant damage to the tiles. The tiles do a fantastic job of repelling heat, however they are very fragile and susceptible to impact damage. Damage numbering up to forty tiles is considered normal on each mission due to ice dropping off of the external tank (ET) and plume re-circulation causing this debris to impact with the tiles. But the extent of damage at the conclusion of this mission was not "normal."

The pattern of hits did not follow aerodynamic expectations, and the number, size and severity of hits were abnormal. Three hundred and eight hits were counted during the inspection, one-hundred and thirty two (132) were greater than one inch. Some of the hits measured fifteen (15) inches long with depths measuring up to one and one-half (1 1/2) inches. Considering that the depth of the tile is two (2) inches, a 75% penetration depth had been reached. Over one hundred (100) tiles have been removed from the Columbia because they were irreparable. The inspection revealed the damage, now the "detective process" began.

During the STS-87 mission, there was a change made on the external tank. Because of NASA's goal to use environmentally friendly products, a new method of "foaming" the external tank had been used for this mission and the STS-86 mission. It is suspected that large amounts of foam separated from the external tank and impacted the orbiter. This caused significant damage to the protective tiles of the orbiter. Foam cause damage to a ceramic tile?! That seems unlikely, however when that foam is combined with a flight velocity between speeds of MACH two to MACH four, it becomes a projectile with incredible damage potential. The big question? At what phase of the flight did it happen and what changes need to be made to correct this for future missions?