Problems loading bootstrap - .htaccess

I have having issues where the .htaccess is prevent the loading on the bootstrap css style sheet. I know its the .htaccess, because if I delete it, and then recreate it, it works. 
This has become an issue for when I change browsers, the style sheet no longer works.

Has anyone else been having this issue?

Code:

.htaccess file 

<IfModule mod_rewrite.c>

RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

html link to style sheet

   <link href="<?php echo base_url(); ?>bootstrap/css/bootstrap.css" rel="stylesheet">