I have a 4 core cpu which I'm not sure if BOINC considers that 1 CPU or 4.
Anyhow I set a limit of 50 % of the CPUs and 2 CPUs which I thought would limit Milkway to 2 cores but clearly one of the tasks says 4 cores and task manager shows its working with all 4. So is Milkyway ignoring the Boinc rules, or is there something I don't understand? Both are likely.

Unhide your computer.

I have a 4 core cpu which I'm not sure if BOINC considers that 1 CPU or 4.
Anyhow I set a limit of 50 % of the CPUs and 2 CPUs which I thought would limit Milkway to 2 cores but clearly one of the tasks says 4 cores and task manager shows its working with all 4. So is Milkyway ignoring the Boinc rules, or is there something I don't understand? Both are likely.

50% in this case does not mean use only two cores, it means only use your cpu cores 50% of the time, if you go into Task Manager, I am assuming you are using Windows but since your pc's are hidden it is only a guess, you will see that your cpu usage is bouncing up and down, but sorta kinda only averaging 50% usage overall. To get Boinc to only use 2 of your 4 cpu cores you need to adjust the line in the Boinc Manager under Tools, computing preferences, the processor usage tab, then the line near the bottom of the page that says "on multi-processor systems, use at most [] % of the processors (zero means no restrictions)". Put 50 in that box and Boinc will not use more than 2 of the 4 cores TOTAL for ANY project, that is not 2 for this project and 2 for some other project, that is TWO CORES TOTAL!! To let Boinc use 3 of your cpu put 75 in the box. Be sure to click the 'ok' box to save the changes.

The Einstein project tasks that I've run never use more than one core each and I've noticed they interpret a 50% CPU limit as 50% per core. So if you suspend two tasks the other two don't ramp their two cores to 100%ish to put the average load at 50%, which I always thought was their loss. A single four core task on MilkyWay is limiting to 50% avg but it seems to ignore the number of cores limit. Either I shouldn't have gotten that task or it should have only run on two. I'm not sure how the tasks are written.
I haven't been running MW long, but have had a couple of single core tasks come through. I just haven't observed their interpretation of the rules.
I was hoping to say here's your two cores Milkyway, and here's your two cores Einstein, but it seems I'll just have to let them run to their own interpretation and see if the task switch time works. What started all this was the four core MW task jumped right in and took over the four cores and set a couple of Einsteins tasks to waiting to run or some verbage. This may be because BOINC manager would have long since seen the task switch timer expire since Einstein was the only thing running. Unless I suspended the MW task there was no way to get it to share. I'll check on it later, if MW doesn't share with the task time switch set, it'll have to go.

I haven't been running MW long, but have had a couple of single core tasks come through. I just haven't observed their interpretation of the rules. I was hoping to say here's your two cores Milkyway, and here's your two cores Einstein, but it seems I'll just have to let them run to their own interpretation and see if the task switch time works.

No Boinc does not allow for that fine of a control by us users.

What started all this was the four core MW task jumped right in and took over the four cores and set a couple of Einsteins tasks to waiting to run or some verbage. This may be because BOINC manager would have long since seen the task switch timer expire since Einstein was the only thing running. Unless I suspended the MW task there was no way to get it to share. I'll check on it later, if MW doesn't share with the task time switch set, it'll have to go.

Some MW units are multi-tasking units and will use all the cores on your cpu that were available to Boinc when you got your last set of tasks from MW. Meaning if you have 4 cpu cores available to Boinc when you get new tasks the tasks will use all 4 of those cores to run those units, not all the time but at some point or points during the units crunching. The non multi-tasking tasks are single cpu core units and will only run on a single cpu core for their entire crunching time. You can adjust which kind you get thru the webpage at Your Account, Miklyway@home preferences:
Run only the selected applications
MilkyWay@Home
MilkyWay@Home N-Body Simulation
Milkyway@Home Separation
Milkyway@Home Separation (Modified Fit)

AND unchecking this box too:
If no work for selected applications is available, accept work from other applications? []

I think the "N-Body Simulation" tasks are the multi cpu core units here.