steps to reproduce:
assuming we got a siteaccess "mysiteaccess" and an active extension "myextension"
1- redeclare an array in a siteaccess ini file for example
settings/mysiteaccess/design.ini.append.php
[StylesheetSettings]
CSSFileList[]
CSSFileList[]=toto.css

2- add a value to this array in an extension settings;
extension/myextension/settings/design.ini.append.php
[StylesheetSettings]
CSSFileList[]=otherfile.css

3- look the results in admin /settings/view
the placement for otherfile.css is marked siteaccess which is incorrect

Explanation:
The parser class (ezini.php) got a BlockValuesPlacement array which store placement.
The problem is the key corresponding to the property is not reinitialized when an array is redelared in an ini file.
This causes an offset compared to the keys stored in BlockValues.

To resolve this problem I propose the following change on ezini.php (line 790)

$this->BlockValuesPlacement[$currentBlock][$varName] = array( $file );

instead of

$this->BlockValuesPlacement[$currentBlock][$varName][] = $file;

after that I got the expected dispançoislay in settings/view.

I checked this on 2012.9 and 2012.4

Hope this helps
Regards

Francois Boukhalfa