It seems to me you are running out of resources and the operations per loop take longer than 1000ms to execute if you acquire so many channels at once.
There are many ways to address this issue: (1) Make sure the acquisition loop does not do any unecessary operation, don't update the front panel (charts, etc) but wait until all data is acquired. If you need a realtime chart, turn off autoscaling and use simple lines instead of fancy dots, etc. (2) Don't use highest level I/O that initialize the entire hardware for each reading. (3) turn off debugging, (4) don't run uneccesary other tasks, e.g. of you have several parallel loops that e.g. monitor front panel activity, make sure they contain at least a 100ms wait. If they don't contain a wait, they suck up CP
U cycles like a sponge while doing nothing. (5) get a faster computer, etc.