FakeVim text is aligned different compared to text written in normal editor

Autoindentation with FakeVim does not appear to be aligning the text the same way as when tabbing text that was written the normal editor.

See the attached screenshot for a detailed look at the problem. The if was created after the alarmManager.addAlarm line. Thus the text went from being

alarmManager.addAlarm(...)

To become

variable++;
if(variable >= 3)
{
    variable = 3;
    alarmManager.addAlarm(...)
}

Now this modification was done in fakevim and the variable = 3; line was indented using FakeVims autoindentation, while I added a manual tab in front of the alarmManager line. These 2 lines should align perfectly above and below each other but they are slightly off relative each other, which can be seen in the screenshot.

My FakeVim settings are:
Automatic indentation
Smart indentation
Highlight search result
Show partial command
Start of line
Pass keys in insert mode
Incremental search
Use wrapscan
Shift width: 4
Tabulator size: 4
Scroll offset: 0
Backspace: indent,eol,start
Read .vimrc.

.vimrc contains the following:
execute pathogen#infect()
syntax on
filetype plugin indent on

set showcmd
set cinoptions+=g0
color wombat256
set noexpandtab
set tabstop=4
set shiftwidth=4

let g:NERDTreeWinPos = "right"
"let Tlist_Auto_Open = 1

nmap <silent> <A-Up> :wincmd k<CR>
nmap <silent> <A-Down> :wincmd j<CR>
nmap <silent> <A-Left> :wincmd h<CR>
nmap <silent> <A-Right> :wincmd l<CR>
nmap <silent> <C-A-Left> :tabprevious<CR>
nmap <silent> <C-A-Right> :tabnext<CR>

map ö ^
map Ö 0

inoremap kj <esc>

autocmd VimEnter * NERDTree
autocmd VimEnter * wincmd p

nnoremap <silent> <F8> :TlistToggle<CR>

My text editor behavior settings:
Tab policy: Tabs only
Tab size: 4
Indent size: 4
Align continuation lines: with regular indent
Enable automatic indentation
Backspace indentation: unindents
Tab key performs auto indent: never
Clean whitespace
Clean indentation
Ensure newline at end of file
Default encoding: UTF-8
UTF-8 BOM: Keep if already present
Enable mouse navigation
Enable scroll wheel zooming
Enable built-in camel case navigation