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Elementary OS 0.4.1
1.0.10
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Bug?
None
Gmail

I'm thinking - does it still count unread messages in the "Trash" folder? If so, exclude it from the counter poll?
I've noticed the same bug and I find it annoying too! What I think is causing this is Mailspring is having trouble recognizing that you have already read the email. Gmail has marked it differently with a label or as important for example so when your read the email itself Mailspring records this but the other labels/ storage architecture of Gmail does not get notified leaving Mailspring to think its all different emails you still haven't opened.
Just my thoughts, hopefully it helps people reproduce this issue and find a solution to it.
I've been having this issue for awhile now and it's quite annoying as I can no longer tell at a glance when new e-mails have arrived. if there is anything I can do to help track this down let me know.
Deleting the account and setting it back is fixing the issue (short term).
Just installed Mailspring, but got similar issue. I have UNREAD emails in many folders but app is not showing any of those as unread - or just number of unread on each of folders (ps. in gmail, I have configured filter to skip Inbox and those messages are going directly to folders)
Created a new folder, and received emails that get filtered directly into this folder. These emails don't show an unread account on the folder itself, nor does Mailspring notify me that an email has come in.
Same issue as @legendary-jld. I'm using my ISP's IMAP server. The ISP's webmail shows correct unread in folders other than inbox.
I'm having the same issue. I'm using gmail accounts and Rebuild Cache option temporarily fixes the problem but it is frustrating to see this issue is open almost for a year now.
OS version: MacOS Mojave 10.14.1
Mailspring version: 1.5.3
same issue for me 1.7.4 / Fedora 31
Most helpful comment
Created a new folder, and received emails that get filtered directly into this folder. These emails don't show an unread account on the folder itself, nor does Mailspring notify me that an email has come in.