Well, I've been tinkering. Would be great to have a setting to double the pixels in window mode, maybe Peter and the gang can make that happen at some point, but to the end of improving the redraw for full screen, I've been playing with the settings.txt file in the data folder.
I have had some some similar issues. I found the fix for most of them today and maybe it will help you, maybe not, but here it is...
On my compaq running Vista, with Athelon X2 CPU and Nvidea GeForce 6150 in window mode, screen redraw and initialization was slow and I had to flip back and forth from the lobby.
On my Sony running Win7, with Intel Pentium Dual-Core and Intel 945 Express in window mode, initilization was slow but worked correctly. It does exhibit the same blinking switching to full screen you described (OS maybe?)
In full screen, both took 15 seconds to switch to and did not rescale, so the graphics were still the same size.
Other than the blinking problem on the Sony, I was able to remedy all issues with the changes to settings.txt in the data folder.
This is the default settings.txt
VERSION 1.3.4
username Unnamed
manualJoinAddress
masterServer
http://www.planetmule.comprimaryKeys 38 40 37 39 32 116 0 0 0 0 0 0 0
secondaryKeys 87 83 65 68 17 0 0 0 0 0 0 0 0
soundOn true
playLoginMusic true
mapSkin default
windowSkin Default
fastAiDevelopment true
vsync 1
useTwoWindows false
useAWTGLCanvas false
ignoreRepaint true
snapFullscreenScale true
bufferStrategy 1
On my Compaq with Nvidea GeForce 6150 video, the following settings work best and fix all bugs (Would note that I had all the same bugs when the Sony Vaio was running Vista that the Compaq currently had, odd being totally different hardware and the only commonality being the OS. Switching to Win7 did the resulted in same thing on my Vaio that happened to you, and while some of these settings speed things up on the Vaio, it did not fix the blinking on fullscreen switch.)
VERSION 1.3.4
username Unnamed
manualJoinAddress
masterServer
http://www.planetmule.comprimaryKeys 38 40 37 39 32 116 0 0 0 0 0 0 0
secondaryKeys 87 83 65 68 17 0 0 0 0 0 0 0 0
soundOn true
playLoginMusic true
mapSkin default
windowSkin RavenGraphiteGlass
fastAiDevelopment false
vsync 1
useTwoWindows false
useAWTGLCanvas true (This fixed the problem that made me have to flip to the lobby.)
ignoreRepaint false (This sped up my redraw everywhere, game starts 3 times faster, and fullscreen switch is lighting fast)
snapFullscreenScale false (Made Fullscreen Actually Fullscreen)
bufferStrategy 1
Try different combinations until you find the one that works best for you. I've made similar adjustments on my Sony Vaio with an Intel 945 Express. I do have to note as stated above, that I have the same blinking problem on the Intel switching to fullscreen after upgrading to Win7 and none of these settings seem to cure it, using the same video driver version as I did in Vista and the Compaq is running Vista and the Sony is running Windows 7, so it might be the OS, and I won't know unless I try Win7 on the compaq, which I am thinking of doing in the near future, so I'll let you know what happens.
Still would love to see rescalable graphics in window mode. That would be awesome.
