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Popping out the softphone from the utility bar certainly does create some odd behaviors, in part because you've now created a separate browser window, and there are limitations on what can be done within the browser to direct focus. Additionally, Salesforce is responsible for the "pop out" feature, and from our testing it appears that multiple tabs of the Salesforce app are not aware of the popped out setting on other tabs, meaning they are re-instantiating the softphone on each page, regardless of whether you've popped out on a separate tab; our client has logic built in to it to run multiple instances of the softphone and coordinate state/status across tabs (this logic prevents things like multiple screen pops on an incoming call, multiple call logs from being created, etc.). This primary tab logic is what results in the call presenting on tab #2 while the agent is viewing tab 2 (the call will also be represented on tab 1 or the popped out window if the agent were to navigate back to it, but the screen pop will be occurring within tab 2, because that was the primary tab when the agent received the conversation).Additionally, there are documented limitations to the number of browser tabs that can be supported due to subscription limits back to the Genesys Cloud platform; if you run over the subscription limits, then topics may behave erratically: https://help.mypurecloud.com/faqs/can-i-run-genesys-cloud-for-salesforce-in-multiple-browser-tabs/.
Using multiple tabs there are also some configuration limits due to the overall architecture of the embedded client; one that must be payed close attention to is the "pop out webRTC" setting. These are also documented on the page I just linked.
Multiple tabs of the lightning experience are also known to put additional resource constraints on the web browser; coupled with recent changes to Chrome that deprioritize/throttle resources on pages that are not in focus, mutli-tab use of an enterprise software application is generally not a recommended practice, especially if other options are available.
In general, we find the majority of our customers using Salesforce lightning running apps with console navigation enabled. This allows multiple records to be displayed as tabs within a single Salesforce page, preventing the need for opening multiple instances of Salesforce, and running only a single instance of the Softphone within the WebRTC frame. Console navigation also allows for multiple related records to be aggregated into a single "workspace" tab; this workspace can then be transferred as an entire conversation context to the next agent in the process, allowing the second agent to receive a screenpop that contains an account, contact, lead, and custom object based on the workspace assembled by the first agent: https://help.mypurecloud.com/articles/workspace-transfers/. I fully recognize the creating a new app within Salesforce is not a trivial undertaking, especially with a large number of users, but this way of working within Salesforce does present a number of substantial benefits, which is why it represents the vast majority of our integration usage.
Every year, Genesys® delivers more than 70 billion remarkable customer experiences for organizations in over 100 countries. Through the power of the cloud and AI, our technology connects every customer moment across marketing, sales and service on any channel, while also improving employee experiences. Genesys pioneered Experience as a ServiceSM so organizations of any size can provide true personalization at scale, interact with empathy, and foster customer trust and loyalty. This is enabled by Genesys Cloud™, an all-in-one solution and the world's leading public cloud contact center platform, designed for rapid innovation, scalability and flexibility. Visit www.genesys.com.