So I have two clients running BES 4.1 for Exchange. One is a new install and is having issues where the mail isn't being deleted automatically back and forth from device to desktop.

The other is an upgrade and is having issues where it syncs the calendar from outlook to handheld but doesn't sync from handheld to outlook. Are there any known issues/fixes for these issues?

We use BES 4.1 for Lotus Domino and had a similar problem.

When I changed the "default" Email Reconciliation setting on my BB 8700, deletions starting working as we wanted.

Try this.

Open Messages on your BB device
Click on the TrackWheel and select options (down near the bottom of the list)
From the Messages Options menu, select Email Reconciliation
Set as follows:
Delete On: Mailbox & Handheld
Wireless Reconcile: On
On Conflicts: Mailbox Wins

Save your changes.

Any future deletions should now sync back and forth.

Hope this helps!

I'd already checked that on the client devices. That setting was already in place.

Delete Desktop[CICAL] and Desktop[SYNC] service books and redo Enteprise Activation if it's easy , that should help

But read/unread synch is not instantanius (sp?) to my knowledge , it usually takes between 5-30+ minutes depending on BES activity.

Check your BESadmin permissions as per the install guide.

Certainly sounds permissions based to me

Exactly, straight away a rights issue.