if there's anything else I can help with let me know

1) you said app acknowledged exit on BOINC quit. It means that at least sometimes flag about exit passed and obeyed. So we need to find out why it's not always passed and/or obeyed. So, try next things:
a) snooze (and look into slot stderr/task manager - will app's process terminates and what delay between your snooze request and process disappearance from task manager's list).
b) snooze GPU (same)
c) suspend project (same)
d) suspend currently executing GPU task (same).

2) as I wrote earlier look into system log - were there any mentions about display driver restarts ?

3) did you configure BOINC to stop all excution on not idle state (user presents /keyboard activity state) or only GPU tasks should stop in this state? Have you any another GPU project active to check if it's only AP issue? Early you said OpenCL (or not?) MB app exits correctly, right ?
(OpenCL MB uses absolutely same style of BOINC critical section handling as OpenCL AP, that's why I'm inclined to consider critical section handling mostly irrelevant to this issue)

EDIT:

seti stops correctly its just astropulse ATI that doesn't

Lets start to be more precise with terminology and distinguish CPU tasks from OpenCL/GPU tasks at least. Both apps are "SETI" in broad sense so perhaps you spoke about SETI MultiBeam (or SETI Enchanced) app. But CPU one or GPU one ?

Do you reserve a CPU core?
I see you are running on AMD FX 8350.
Especially on high blanked APs this CPU gets unresponsive if no core is freed.