David,
FieldPoint RT Controllers have two programs running simultaneously; the LabVIEW Run-Time Engine and the IA Control Environment. These two programs must share access to the processor and to the inter-module communication bus. When your embedded program uses the FP Read.vi, it causes a read action to take place on the bus to read from the shared memory of the IO module. The host program, using a FP Read.vi (for ethernet targets), will read from a locally cached copy of the data. The cache is constantly updated on change by the IA control environment. Because both programs are sharing processor time and bus access, they do have an effect on each other. There are a number of ways to control the priority and rates of the control environment and your LabVIEW application. Without knowing how much processing power your embedded LabVIEW application is requiring, it is hard to say how much (if any) effect the host program monitoring will have on the embedded system. The IA Control Environment will typically run at the same or lower priority than the LabVIEW application, so it probably will have little effect.
Regarding the +/- 1 ms timestamp jitter, this is not entirely unexpected. The FP-AI-100 module has an All Channel Update Rate of 2.8 ms. Thus, channel updates are occuring at 2.8 ms intervals, which means that a 1 ms resolution time stamp will show some jitter over time.
Regards,
Aaron
LabVIEW Champion, CLA, CPI