I have has a very similar problem while running the DP scrpt. Although I have 3 processes running at once. The evidence it then using top in terminal i see FAH's running at once and when I look at the .txt file I see:
[07:49:15] + Processing work unit
[07:49:15] Core required: FahCore_78.exe
[07:49:15] Core found.
[07:49:15] Working on Unit 00 [June 6 07:49:15]
[07:49:15] + Working ...
[07:49:15]
[07:49:15] *------------------------------*
[07:49:15] Folding@home Gromacs Core
[07:49:15] Version 1.65 (May 6, 2004)
[07:49:15]
[07:49:15] Preparing to commence simulation
[07:49:15] - Looking at optimizations...
[07:49:15] - Created dyn
[07:49:15] - Files status OK
[07:49:15] - Expanded 197137 -> 951793 (decompressed 482.8 percent)
[07:49:15] - Starting from initial work packet
[07:49:15]
[07:49:15] Project: 1060 (Run 0, Clone 63, Gen 4)
[07:49:15]
[07:49:15] Assembly optimizations on if available.
[07:49:15] Entering M.D.
[07:49:22] Protein: p1060_A21nat_273_99
[07:49:22]
[07:49:22] Writing local files
[07:49:22] Testing CPU type...
[07:49:22] Done testing.
[07:49:22] Extra AltiVec boost OK.
[07:49:22] Writing local files
[07:49:22] Completed 0 out of 2500000 steps (0)
[08:28:15] Writing local files
[08:28:15] Completed 25000 out of 2500000 steps (1)
[09:07:03] Writing local files
[09:07:04] Completed 50000 out of 2500000 steps (2)
[09:45:54] Writing local files
[09:45:54] Completed 75000 out of 2500000 steps (3)
[09:47:57] Writing local files
[09:47:58] Completed 5000 out of 500000 steps (1)
[10:24:45] Writing local files
[10:24:45] Completed 100000 out of 2500000 steps (4)
[11:03:35] Writing local files
[11:03:35] Completed 125000 out of 2500000 steps (5)
[11:42:22] Writing local files
[11:42:22] Completed 150000 out of 2500000 steps (6)
[12:21:09] Writing local files
[12:21:09] Completed 175000 out of 2500000 steps (7)
[12:59:56] Writing local files
[12:59:56] Completed 200000 out of 2500000 steps (8)
[13:00:19] Writing local files
[13:00:19] Completed 10000 out of 500000 steps (2)
[13:38:46] Writing local files
[13:38:46] Completed 225000 out of 2500000 steps (9)
[14:17:30] Writing local files
[14:17:30] Completed 250000 out of 2500000 steps (10)
[14:56:25] Writing local files
[14:56:25] Completed 275000 out of 2500000 steps (11)
[15:35:20] Writing local files
[15:35:20] Completed 300000 out of 2500000 steps (12)
[16:12:46] Writing local files
[16:12:47] Completed 15000 out of 500000 steps (3)
[16:14:13] Writing local files
[16:14:13] Completed 325000 out of 2500000 steps (13)
[16:53:06] Writing local files
[16:53:06] Completed 350000 out of 2500000 steps (14)
[17:36:30] Writing local files
[17:36:31] Completed 375000 out of 2500000 steps (15)
You can see that there appears to be two running on one processor. The .txt for my other porcessor appears to be fine.