I have a Toshiba M200 tablet with the same problem.  Is this is a kernel
problem rather than a Wacom driver problem.  The digitizer in the M200
is a serial device (I think that's true on the Thinkpad X41/X60 tablets,
too).

When initially booting the system, the digitizer's serial port is
detected: (dmesg output below)

[   22.207011] Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing 
enabled
[   22.207940] 00:09: ttyS0 at I/O 0x338 (irq = 4) is a 16550A

The pen works fine, until I suspend.  After resuming, the pen fails, and
dmesg starts spitting out these errors:

[ 1024.204000] ttyS0: LSR safety check engaged!
[ 1024.204000] ttyS0: LSR safety check engaged!
[ 1024.204000] ttyS0: LSR safety check engaged!

Googling that message seems to indicate that the reason the pen no
longer works is that the serial port is no longer being detected after
the resume.  The same thing happens with hibernate  -a dead serial port
/ pen on resume.

-- 
Pen no longer works after resuming from suspend
https://bugs.launchpad.net/bugs/108961
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