In Tools -> Computing preferences... -> disk and memory usage tab, "Leave applications in memory while suspended" is unchecked (leave_apps_in_memory set to 0). As of previous version(and continuing into the current version), the application processes remain loaded in memory when BOINC computation is suspended due to computer usage (run_if_user_active set to 0). I have performed "Read local prefs file".

BOINC 7.0.28 (x86)
Windows XP Media Center Edition Version 2002 Service Pack 3

global_prefs.xml:
<global_preferences>
<source_project>http://setiathome.berkeley.edu/</source_project>
<source_scheduler>http://setiboinc.ssl.berkeley.edu/sah_cgi/cgi</source_scheduler>
<mod_time>1219240727</mod_time>
<run_if_user_active/>
<idle_time_to_run>3</idle_time_to_run>
<suspend_if_no_recent_input>0</suspend_if_no_recent_input>
<cpu_scheduling_period_minutes>60</cpu_scheduling_period_minutes>
<work_buf_min_days>0</work_buf_min_days>
<work_buf_additional_days>3</work_buf_additional_days>
<max_cpus>2</max_cpus>
<max_ncpus_pct>100</max_ncpus_pct>
<cpu_usage_limit>100</cpu_usage_limit>
<disk_interval>60</disk_interval>
<disk_max_used_gb>100</disk_max_used_gb>
<disk_max_used_pct>50</disk_max_used_pct>
<disk_min_free_gb>0.001</disk_min_free_gb>
<vm_max_used_pct>30</vm_max_used_pct>
<ram_max_used_busy_pct>50</ram_max_used_busy_pct>
<ram_max_used_idle_pct>90</ram_max_used_idle_pct>
<max_bytes_sec_down>0</max_bytes_sec_down>
<max_bytes_sec_up>0</max_bytes_sec_up>
<venue name="home">
<run_on_batteries/>
<run_if_user_active/>
<idle_time_to_run>2</idle_time_to_run>
<suspend_if_no_recent_input></suspend_if_no_recent_input>
<cpu_scheduling_period_minutes>60</cpu_scheduling_period_minutes>
<hangup_if_dialed/>
<work_buf_min_days>0</work_buf_min_days>
<work_buf_additional_days>3</work_buf_additional_days>
<max_cpus>16</max_cpus>
<max_ncpus_pct>100</max_ncpus_pct>
<cpu_usage_limit>100</cpu_usage_limit>
<disk_interval>60</disk_interval>
<disk_max_used_gb>100</disk_max_used_gb>
<disk_max_used_pct>50</disk_max_used_pct>
<disk_min_free_gb>0.001</disk_min_free_gb>
<vm_max_used_pct>75</vm_max_used_pct>
<ram_max_used_busy_pct>50</ram_max_used_busy_pct>
<ram_max_used_idle_pct>90</ram_max_used_idle_pct>
<max_bytes_sec_down>0</max_bytes_sec_down>
<max_bytes_sec_up>0</max_bytes_sec_up>
</venue>
</global_preferences>

global_prefs_override.xml:
<global_preferences>
<run_on_batteries>0</run_on_batteries>
<run_if_user_active>0</run_if_user_active>
<run_gpu_if_user_active>0</run_gpu_if_user_active>
<idle_time_to_run>0.500000</idle_time_to_run>
<suspend_cpu_usage>25.000000</suspend_cpu_usage>
<start_hour>15.000000</start_hour>
<end_hour>15.000000</end_hour>
<net_start_hour>0.000000</net_start_hour>
<net_end_hour>0.000000</net_end_hour>
<leave_apps_in_memory>0</leave_apps_in_memory>
<confirm_before_connecting>0</confirm_before_connecting>
<hangup_if_dialed>0</hangup_if_dialed>
<dont_verify_images>0</dont_verify_images>
<work_buf_min_days>0.000000</work_buf_min_days>
<work_buf_additional_days>2.000000</work_buf_additional_days>
<max_ncpus_pct>95.000000</max_ncpus_pct>
<cpu_scheduling_period_minutes>60.000000</cpu_scheduling_period_minutes>
<disk_interval>60.000000</disk_interval>
<disk_max_used_gb>10.000000</disk_max_used_gb>
<disk_max_used_pct>20.000000</disk_max_used_pct>
<disk_min_free_gb>1.000000</disk_min_free_gb>
<vm_max_used_pct>30.000000</vm_max_used_pct>
<ram_max_used_busy_pct>10.000000</ram_max_used_busy_pct>
<ram_max_used_idle_pct>90.000000</ram_max_used_idle_pct>
<max_bytes_sec_up>0.000000</max_bytes_sec_up>
<max_bytes_sec_down>0.000000</max_bytes_sec_down>
<cpu_usage_limit>80.000000</cpu_usage_limit>
<daily_xfer_limit_mb>0.000000</daily_xfer_limit_mb>
<daily_xfer_period_days>0</daily_xfer_period_days>
</global_preferences>

Appears to be working now. Maybe it takes some period of time before the local preferences are loaded and used?

Normally local preferences are used immediately after saving them through the GUI. However, if you hand-edit the global_prefs_override.xml file and only restart BOINC later, the new prefs will also only be used later.

There is one thing though: As long as an application hasn't made a checkpoint yet, it will stay in memory, unless you exit BOINC completely. There are still applications out there that don't checkpoint, at all. So they'll run start to finish, with all pauses in between, with apps staying in memory.

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