After latest update total system slowdown

After installing the latest security update my system has slowed dramatically. The mouse pointer is jerky and sound stops and starts every operation has a time lag.
I've repaired the permissions but this hasn't helped.
Anybody else have this issue or know how to fix it?

Also when I try and repair permissions I get this:
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Warning: SUID file "usr/bin/at" has been modified and will not be repaired.
Warning: SUID file "usr/bin/atq" has been modified and will not be repaired.
Warning: SUID file "usr/bin/atrm" has been modified and will not be repaired.
Warning: SUID file "usr/bin/batch" has been modified and will not be repaired.
Warning: SUID file "usr/bin/chfn" has been modified and will not be repaired.
Warning: SUID file "usr/bin/chpass" has been modified and will not be repaired.
Warning: SUID file "usr/bin/chsh" has been modified and will not be repaired.
Permissions differ on "usr/share/man/man1/atq.1.gz", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "usr/share/man/man1/atrm.1.gz", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "usr/share/man/man1/batch.1.gz", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "usr/share/man/man8/halt.8.gz", should be -r--r--r-- , they are lr--r--r-- .
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/lib/jvm.cfg", should be 0, user is 95.
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Libraries/classlist" , should be 0, user is 95.
Permissions differ on "usr/X11R6", should be lrwxr-xr-x , they are drwxr-xr-x .
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
ACL found but not expected on "Library".
Any ideas?

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--------- beginning of /dev/log/main
I/dalvikvm(24476): Enabling JNI app bug workarounds for target SDK version 11...
D/dalvikvm(24476): GC_CONCURRENT freed 174K, 2% free 17054K/17264K, paused 2ms+2ms, total 15ms
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W/ViewRootImpl(24476): Dropping event due to root view being removed: MotionEvent { action=ACTION_UP, id[0]=0, x[0]=38.0, y[0]=-115.0, toolType[0]=TOOL_TYPE_FINGER, buttonState=0, metaState=0, flags=0x0, edgeFlags=0x0, pointerCount=1, historySize=0, eventTime=27743086, downTime=27743066, deviceId=4, source=0x1002 }
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I/dalvikvm-heap(24476): Grow heap (frag case) to 17.615MB for 328336-byte allocation
D/dalvikvm(24476): GC_FOR_ALLOC freed 0K, 2% free 18010K/18252K, paused 8ms, total 8ms
D/dalvikvm(24476): GC_FOR_ALLOC freed <1K, 2% free 18011K/18252K, paused 9ms, total 9ms
I/dalvikvm-heap(24476): Grow heap (frag case) to 18.073MB for 479536-byte allocation
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D/dalvikvm(24476): GC_FOR_ALLOC freed 3411K, 14% free 24528K/28204K, paused 12ms, total 13ms
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(99382)

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