So I installed PS:T on my MacBook a couple of days ago with all the recommended mods and it was running acceptably well. It occasionally crashed for seemingly no reason, but I could live with that. This morning, after one such crash, when I restarted the game, the entire program started constantly flickering black, so much that it is nearly impossible to see the display. Oddly, if I hit volume up/down, brightness up/down, or anything else that brings up a Mac display over the game screen, the flickering stops for as long as the Mac display is showing, then it goes back to flickering.

I have updated Wineskin and my wrapper and tried change the display settings, but it doesn't seem to change anything.

My last runlog says:

user.reg is not a valid registry file
fixme:win:EnumDisplayDevicesW ((null),0,0x32a2ac,0x00000000), stub!
fixme:d3d_surface:surface_cpu_blt Filter WINED3D_TEXF_LINEAR not supported in software blit.
fixme:ddraw:ddraw_surface7_Flip Ignoring flags 0x1.
fixme:d3d_surface:surface_cpu_blt Filter WINED3D_TEXF_LINEAR not supported in software blit.

Any thoughts on how to fix this?

There might be something wrong with the wrapper or its configuration or an interfering application. First of all check the steps in the Common troubleshooting.

Copying the game from the DMG file makes the new version work fine, but doesn't do anything to the bugged existing version. Oh well, I guess I will reinstall everything and start over.

After reinstalling everything, I am back to the original problem of random crashes.

WineskinX11: main(): argc=12
Waiting for startup parameters via Mach IPC.
WineskinX11: do_start_x11_server(): argc=12
Attempting to use pixel depth of 24
[1744872.327] WineskinX11 starting:
[1744872.327] X.Org X Server 1.13.0
[1744872.327] Build Date: 20120921
[1744872.328] _XSERVTransmkdir: ERROR: euid != 0,directory /tmp/.X11-unix will not be created.
[1744872.349] Initializing built-in extension Generic Event Extension
[1744872.349] Initializing built-in extension SHAPE
[1744872.349] Initializing built-in extension MIT-SHM
[1744872.349] Initializing built-in extension XInputExtension
[1744872.349] Initializing built-in extension XTEST
[1744872.349] Initializing built-in extension BIG-REQUESTS
[1744872.349] Initializing built-in extension SYNC
[1744872.349] Initializing built-in extension XKEYBOARD
[1744872.349] Initializing built-in extension XC-MISC
[1744872.349] Initializing built-in extension XINERAMA
[1744872.349] Initializing built-in extension PseudoramiX
[1744872.349] Initializing built-in extension XFIXES
[1744872.349] Initializing built-in extension RENDER
[1744872.349] Initializing built-in extension RANDR
[1744872.349] Initializing built-in extension DAMAGE
[1744872.349] Initializing built-in extension MIT-SCREEN-SAVER
[1744872.349] Initializing built-in extension DOUBLE-BUFFER
[1744872.349] Initializing built-in extension RECORD
[1744872.349] Initializing built-in extension X-Resource
[1744872.349] Initializing built-in extension XVideo
[1744872.349] Initializing built-in extension XVideo-MotionCompensation
[1744872.349] Initializing built-in extension GLX
[1744872.350] x: 0, y: 0, w: 1440, h: 878
[1744872.700] (II) GLX: Initialized Core OpenGL GL provider for screen 0
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/75dpi, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/100dpi, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/cyrillic, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/misc, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/OTF, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/Speedo, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/TTF, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/Type1, removing from list!
[1744872.702] [dix] Could not init font path element /opt/X11/share/fonts/util, removing from list!
[1744874.804] noPseudoramiXExtension=0, pseudoramiXNumScreens=1
Engine Used: WS9Wine1.7.14
Hardware:

Hardware Overview:

Model Name: MacBook Pro
Model Identifier: MacBookPro4,1
Processor Name: Intel Core 2 Duo
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache: 3 MB
Memory: 2 GB
Bus Speed: 800 MHz
Boot ROM Version: MBP41.00C1.B03
SMC Version (system): 1.27f3
Sudden Motion Sensor:
State: Enabled

Graphics/Displays:

NVIDIA GeForce 8600M GT:

Chipset Model: GeForce 8600M GT
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 256 MB
Vendor: NVIDIA (0x10de)
Device ID: 0x0407
Revision ID: 0x00a1
ROM Revision: 3212
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900
Pixel Depth: 32-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Built-In: Yes

fixme:win:EnumDisplayDevicesW ((null),0,0x32a5f4,0x00000000), stub!
fixme:d3d_surface:surface_cpu_blt Filter WINED3D_TEXF_LINEAR not supported in software blit.
fixme:ddraw:ddraw_surface7_Flip Ignoring flags 0x1.
fixme:d3d_surface:surface_cpu_blt Filter WINED3D_TEXF_LINEAR not supported in software blit.

Have you updated your graphics drivers yet? Also try installing the game under a new user account, to see if the crashes derive from a conflicting software under your current account.