If this happens too often,  uncheck everything but "UI Prompt" in

Preferences/General/Security/Secure Storage/Master password providers

Then delete storage on Contents tab.

Atelier will create a master password and will ask you for it on every startup. This is annoying,  but sometimes better than having to recreate connections from scratch.

Thank you for reporting.

This is a known issue that is planned to be fixed in Atelier 1.1. (May be available earlier in beta)

I've just reproduced the issue on "Cache for Windows (x86-64) 2017.2 (Build 671.0U QDTESTSYS) Tue May 9 2017 20:44:20 EDT"

POST http://192.168.2.178:57775/api/atelier/v1/SAMPLES/docs
Accept: application/json
Content-Type: application/json
["%Library.String.cls", "lookup1.mac"]
 -- response --
200 OK
Date:  Wed, 10 May 2017 12:57:58 GMT
Server:  Apache
Cache-Control:  no-cache
Expires:  Thu, 29 Oct 1998 17:04:19 GMT
Pragma:  no-cache
Transfer-Encoding:  chunked
Content-Encoding:  gzip
Keep-Alive:  timeout=120
Connection:  Keep-Alive
Content-Type:  application/json; charset=utf-8

{
    "status": {
        "errors": [],
        "summary": ""
    },
    "console": [],
    "result": {
        "content": [
            {
                "name": "%Library.String.cls",
                "db": "CACHELIB",
                "ts": "2017-05-09 20:31:58.000",
                "upd": true,
                "cat": "CLS",
                "status": "",
                "enc": false,
                "content": [
                    "IncludeGenerator %occUtility",
                    "",
                    "/// The %String data type class represents a string.",
                     ....
                ],                "console": []
            },
            {
                "name": "lookup1.mac",
                "db": "SAMPLES",
                "ts": "2002-01-03 12:07:15.000",
                "upd": true,
                "cat": "RTN",
                "status": "ОШИБКА #5001: Missing Source for Document: lookup1.MAC",
                "enc": false,
                "content": "",
                "console": []
            }
        ]
    }
}

Thank you for reporting, Atelier team will look into this.

Hello. Could you please check "Problems" view to see if it has a description for the error marker?