Running :PlugClean or :PlugInstall in gVim launches several pop-under windows which adversely affect performance on Windows.

The same does not happen for console Vim and works as intended. I'm not entirely sure anything can be done about this, however, I decided to open a ticket anyways.
VIM - Vi IMproved 8.0 (2016 Sep 12, compiled Nov 11 2016 21:50:00)
MS-Windows 64-bit console version
Included patches: 1-76
Compiled by hp@HP-PC
Huge version without GUI. Features included (+) or not (-):
+acl +ex_extra -mouseshape +tag_old_static
+arabic +extra_search +multi_byte -tag_any_white
+autocmd +farsi +multi_lang +tcl/dyn
-balloon_eval +file_in_path +mzscheme/dyn +termguicolors
-browse +find_in_path -netbeans_intg -tgetent
++builtin_terms +float +num64 -termresponse
+byte_offset +folding +packages +textobjects
+channel -footer +path_extra +timers
+cindent +gettext/dyn +perl/dyn +title
+clientserver -hangul_input +persistent_undo -toolbar
+clipboard +iconv/dyn -postscript +user_commands
+cmdline_compl +insert_expand +printer +vertsplit
+cmdline_hist +job +profile +virtualedit
+cmdline_info +jumplist +python/dyn +visual
+comments +keymap +python3/dyn +visualextra
+conceal +lambda +quickfix +viminfo
+cryptv +langmap +reltime +vreplace
+cscope +libcall +rightleft +wildignore
+cursorbind +linebreak +ruby/dyn +wildmenu
+cursorshape +lispindent +scrollbind +windows
+dialog_con +listcmds +signs +writebackup
+diff +localmap +smartindent -xfontset
+digraphs +lua/dyn +startuptime -xim
-dnd +menu +statusline -xpm_w32
-ebcdic +mksession -sun_workshop -xterm_save
+emacs_tags +modify_fname +syntax
+eval +mouse +tag_binary
system vimrc file: "$VIM\vimrc"
user vimrc file: "$HOME\_vimrc"
2nd user vimrc file: "$HOME\vimfiles\vimrc"
3rd user vimrc file: "$VIM\_vimrc"
user exrc file: "$HOME\_exrc"
2nd user exrc file: "$VIM\_exrc"
defaults file: "$VIMRUNTIME\defaults.vim"
Compilation: cl -c /W3 /nologo -I. -Iproto -DHAVE_PATHDEF -DWIN32 -DFEAT_CSCOPE -DFEAT_JOB_CHANNEL -DWINVER=0x0501 -D_WIN32_WINNT=0x0501 /Fo.\ObjCULYHTRZAMD64/ -DHAVE_STDINT_H /Ox /GL -DNDEBUG /Zl /MT -DFEAT_MBYTE -DDYNAMIC_ICONV -DDYNAMIC_GETTEXT -DFEAT_TCL -DDYNAMIC_TCL -DDYNAMIC_TCL_DLL=\"tcl86.dll\" -DDYNAMIC_TCL_VER=\"8.6\" -DFEAT_LUA -DDYNAMIC_LUA -DDYNAMIC_LUA_DLL=\"lua53.dll\" -DFEAT_PYTHON -DDYNAMIC_PYTHON -DDYNAMIC_PYTHON_DLL=\"python27.dll\" -DFEAT_PYTHON3 -DDYNAMIC_PYTHON3 -DDYNAMIC_PYTHON3_DLL=\"python35.dll\" -DFEAT_MZSCHEME -I "C:\Users\hp\Desktop\racket-x64\include" -DDYNAMIC_MZSCHEME -DDYNAMIC_MZSCH_DLL=\"libracketxxxxxxx.dll\" -DDYNAMIC_MZGC_DLL=\"libmzgcxxxxxxx.dll\" -DFEAT_PERL -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -DDYNAMIC_PERL -DDYNAMIC_PERL_DLL=\"perl524.dll\" -DFEAT_RUBY -DDYNAMIC_RUBY -DDYNAMIC_RUBY_VER=23 -DDYNAMIC_RUBY_DLL=\"x64-msvcrt-ruby230.dll\" -DFEAT_HUGE /Fd.\ObjCULYHTRZAMD64/ /Zi
Linking: link /RELEASE /nologo /subsystem:console /LTCG:STATUS oldnames.lib kernel32.lib advapi32.lib shell32.lib gdi32.lib comdlg32.lib ole32.lib uuid.lib /machine:AMD64 /nodefaultlib libcmt.lib user32.lib /nodefaultlib:lua53.lib /STACK:8388608 /nodefaultlib:python27.lib /nodefaultlib:python35.lib "C:\TCL\lib\tclstub86.lib" WSock32.lib /PDB:vim.pdb -debug
Running
:PlugCleanor:PlugInstallin gVim launches several pop-under windows which adversely affect performance on Windows.The same does not happen for console Vim and works as intended. I'm not entirely sure anything can be done about this, however, I decided to open a ticket anyways.