Latency questions

No matter what I set it to Axis will always complain that the max latency has been reached. When I run the latency tool is sits at about 20,000 for quite a while and has to odd spike of 60k. Yet Axis reports a latency check immediately, and every time. I have never measured a latency of > 70k and that's with a 1 hour check while hammering the computer (e.g. compiling the kernel), yet with latency set to 80k in the ini file Axis complains immediately. This is with LinuxCNC up to date (as of today) on the master branch.

Any ideas as to why it has this behaviour?

if you pst here your ini and hal we can take a lok at it
in ini file
[EMCMOT]
BASE_PERIOD = 100000

[TRAJ]
DEFAULT_VELOCITY = 10
MAX_LINEAR_VELOCITY = 40

[AXIS_0]
TYPE = LINEAR
HOME = 0.0
FERROR = 1
MIN_FERROR = 0.05
MAX_VELOCITY = 40
MAX_ACCELERATION = 120.0
STEPGEN_MAXACCEL = 200.0
# these are in nanoseconds
DIRSETUP = 10000
DIRHOLD = 10000
STEPLEN = 5000
STEPSPACE = 5000

try this then we get a better look at it

Here is the ini and hal files.

Can you try testing the machine using one of the live Linuxcnc ISOs?
(We don't really know if there is a problem with your Gentoo real time kernel or if it is something in your hardware or it's configuration.)