I believe there was a change for the 2009 model year to fix this issue. Apparently (from what I remember) they changed the material of the header bar to prevent it from warping and allowing the wind noise.
Here is the TSB:
NUMBER: 23-010-09 REV. A
DATE: July 01, 2009
THIS BULLETIN SUPERSEDES TECHNICAL SERVICE BULLETIN 23-010-09, DATED APRIL 17, 2009, WHICH SHOULD BE REMOVED FROM YOUR FILES. ALL REVISIONS ARE HIGHLIGHTED WITH **ASTERISKS** AND INCLUDE LABOR OPERATION NUMBER CHANGES.
Soft Top - Wind Like Sound at Header
This bulletin involves replacing the Header Seal Plate with a new design.
2007 - 2009 (JK) Wrangler
NOTE :This bulletin applies to vehicles equipped with a Soft Top (sales code VJO) built before March 2, 2009 (MDH 0302XX).
The customer may experience a wind-like sound at the Windshield to Soft Top Header.
The condition may be due to the header seal plate warping.
1. Verify that the top is correctly installed and fastened to the vehicle. The soft top cover should be located and clamped in the correct sequence as described in the Owners Manual (DealerCONNECT > TechCONNECT > Owner Manuals or Jeep.com > For Owners > Servicing and Operating My Vehicle > Owner/Service Manuals)
2. Is If the source of the wind like sound coming from the windshield header?
a. YES >> Perform the Repair Procedure
b. NO >> Further diagnosis is required, this bulletin does not apply.
1. Release and fold back the soft top to the vehicle. It is important to roll back the soft top in the sequence referenced in the Owners Manual (DealerCONNECT > TechCONNECT > Owner Manuals or Jeep.com > For Owners > Servicing and Operating My Vehicle > Owner/Service Manuals). Release the soft top from the windshield header and fold back as shown in (Fig 1) following the steps in the owners manual.
2. Carefully remove the screws at each end (side) of the header seal plate (Fig. 2)
NOTE :When removing the screws remember their locations because they will differ in size and style.
3. Remove screws under the flange on the left and right sides as shown in (Fig. 3).
4. Remove the two screws on the upper header assembly from both sides as shown in (Fig. 4).
5. Remove the header assembly and all remaining fasteners as shown in (Fig. 5).
6. Remove windshield header seal plate from the soft top.
7. Feed the soft top material onto the lower header using masking tape to assure proper placement as shown in (Fig. 6).
8. Install the new header seal plate by installing fasteners from the center outward as shown in (Fig. 7).
9. Re-secure the header to the support rods in reverse of the removal process as shown from Step # 4 to Step # 2.
10. Raise and install the soft top to the vehicle. It is important to install the soft top in the correct installation sequence as referenced in the Owners Manual (DealerCONNECT > TechCONNECT > Owner Manuals or Jeep.com > For Owners > Servicing and Operating My Vehicle > Owner/Service Manuals).
11. Verify the soft top is properly secured against the header seal.
Reimbursable within the provisions of the warranty.