How can I prevent mutt to delete random mails (imap box)?

It is a really big problem with mutt:

mutt 1.5.24-1build1
mutt-patched 1.5.24-1build1

with following configuration for a single imap mailbox:

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   set sort=threads
set sort_browser=date
set sort_aux=reverse-last-date-received

set editor="vim"
set edit_headers # See the headers when editing
set autoedit # Go straight to editing; don't prompt for recipients
set forward_format="Fwd: %s" # traditional Fwd: subject
set attribution="On %{\%a, %d %b %Y %H:%M:%S %z}, %n wrote:"

set sidebar_width=30
set sidebar_visible=yes
set sidebar_delim_chars = '/'

color sidebar_new yellow default

bind index,pager \Cp sidebar-prev
bind index,pager \Cn sidebar-next
bind index,pager \Co sidebar-open
bind index l display-message
macro index b '<enter-command>toggle sidebar_visible<enter>'
macro pager b '<enter-command>toggle sidebar_visible<enter>'

set status_format=" %r %b %f %n Del %d Msgs %m %l %%> (%P)"
set pager_format="[%4C/%4m] (%S%Z) %%=%N $i %%> [%lL]"
set date_format="!%H:%M %a %d %b "
set index_format="%4C %Z %[%b%d] %-15.15F %s"
set folder_format="%2C %t %8s %d %N %f"

set record="+Sent"
set copy=yes
set include=yes #quote msg in reply
set fast_reply=yes #no prompting on reply
set beep=no #no noise
set markers=no #no + on wrapped lines
set to_chars=" +TCF" #no L for mail_list
--------------------------------------------

The problem:

I mark a single email I want to delete by d key, there is 55 emails in the folder. Then I open another folder ^o, then I press y to approve remove of the emails and there is about 48 emails in the folder. It removes a lot of emails, I'm not sure they are random, and they are not in the same thread. It looks like if I mark 2nd email from the top of the emails list,it will remove first email and marked by D email too .

Any ideas how to fix it ?