Same here. We upgraded to LDMS 9.5 SP2 because we saw this issue under LDMS 9.0 and we are still seeing this issue. This is a huge issue for us as it is preventing us from deployment any large deployments or anything that requires the user to close applications before the install begins.
Seems there are two docs for this:
http://community.landesk.com/support/docs/DOC-30159 -> saying that it is not fixed
http://community.landesk.com/support/docs/DOC-31027 -> saying that it is fixed (which is obviously not correct).
Glad to see my company is not the only one suffering with this.