Password – Clear Cached GPG Password

If you are using gpg-agent all passwords (including the master password) are stored/saved in ~/.password-store.

From the "pass" website:

There will be a nice password input dialog using the standard gpg-agent (which can be configured to stay authenticated for several minutes), since all passwords are encrypted.

gpg-agent manual page:

--default-cache-ttl n  Set the time a cache entry is valid to n seconds.       
The default is 600 seconds. 

--default-cache-ttl-ssh n Set the time a cache entry used for SSH keys 
is valid to n seconds. 
The default is 1800 seconds. 

--max-cache-ttl n  Set the maximum time a cache entry is valid to n seconds. 

After this time a cache entry will be expired even if it has been accessed recently. 
The default is 2 hours (7200 seconds). 

--max-cache-ttl-ssh n Set the maximum time a cache entry used for SSH keys is valid 
to n seconds. After this time a cache entry will be expired even if 
it has been accessed recently. 
The default is 2 hours (7200 seconds). 

and ...

gpg-agent.conf

This is the standard configuration file read by gpg-agent on startup. It may contain any valid long option; the leading two dashes may not be entered and the option may not be abbreviated. This file is also read after a SIGHUP however only a few options will actually have an effect. This default name may be changed on the command line (see: [option --options]). You should backup this file.

This will only be read if you actually use gpg-agent. If it is "seahorse" (the default in Ubuntu) gpg-agent is ignored).

So you can put any of the 4 parameters in the configuration file with a time in seconds to keep password valid (that includes the master password since that is also stored in ). To release the passwords you can use echo RELOADAGENT | gpg-connect-agent (see the manual for more options).

I had a similar problem and solved it by installing pinentry-gnome3 (I'm using Gnome Shell, not Unity):

sudo apt-get install pinentry-gnome3