My biggest complaint from end-users after upgrading their clients from 5.0.10 to 6.0.1 is about these Notes Security Alerts (ECL). They are for “no signature”! Why are the left-hand bookmarks not signed? I’m referring to the mail, calendar, Domino Designer, etc., links along the left-hand side of the screen. Is this part of welcome.nsf? Did Lotus forget to sign all the design elements in the templates?
Subject: Notes Security Alerts after upgrades - no signature
I’m battling a similar problem. I recently recertified my main development ID, which is used for signing app designs at various levels across the entire worldwide organization, and now users are getting hit with “no signature” ECL alerts the second time they go into their mail files - as if the first access has somehow corrupted the design elements’ signatures. Nightmare 
Subject: RE: Notes Security Alerts after upgrades - no signature
For design elements, signing the database with a trusted ID in ND6 seems to help. At least that is what I did. We have a mixed R5/ND6 environment, and new designs of the database done in the R5 designer had ESAs appearing on ND6 clients. After signing the whole database in the ND6 admin client, the ESAs seemed to have disappeared.
But it seems that I’m facing now a even more disgusting ECL-problem: the database which I still design in R5 (and which I will sign with ND6 prior to any new rollouts) has documents with embedded objects in them. When I try to touch them with LotusScript, an ESA pops up with “-No signature-” on “OLE Object Activation”. Clicking on “More Info…” reveals that it’s not an unsigned design document Notes is nagging about, but rather the very Notes document itself where the OLE object is stored in. Signing all documents in the database with a signer ID seems not to be an option…
Has anybody else an idea what to do?